ajseq.c

Datatypes: AjPSeq AjPSeqall AjPSeqset AjPStr AjPSeqCvt AjPSeqDate AjPSeqDesc AjPList AjPSeqSubdesc AjPList AjPSeqGene AjPList AjPSeqXref AjPList AjPSeqRef AjPList AjPStr

Datatype: AjPSeq

Sequence

Sections: constructors destructors modifiers process element retrieval testing properties conversion calculated properties exit debug

All constructors return a new sequence by pointer. It is the responsibility of the user to first destroy any previous sequence. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions: ajSeqNew ajSeqNewNameC ajSeqNewNameS ajSeqNewRangeC ajSeqNewRangeS ajSeqNewRes ajSeqNewSeq

Function ajSeqNew

Creates and initialises a sequence object.

Synopsis

Prototype

AjPSeq ajSeqNew (
      void
);

Type Name Read/Write Description

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
AjPSeq		RETURN	New sequence object.

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object.

Availability

In release 6.4.0

Function ajSeqNewNameC

Creates and initialises a sequence object with a specified existing sequence as a char

Synopsis

Prototype

AjPSeq ajSeqNewNameC (
      const char* txt,
      const char* name
);

Type Name Read/Write Description

const char* txt Input Sequence string

const char* name Input Sequence name

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
const char*	txt	Input	Sequence string
const char*	name	Input	Sequence name
AjPSeq		RETURN	New sequence object.

Input

txt:	(Input)	Sequence string
name:	(Input)	Sequence name

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object with a specified existing sequence as a char

Availability

In release 6.4.0

Function ajSeqNewNameS

Creates and initialises a sequence object with a specified existing sequence as a string

Synopsis

Prototype

AjPSeq ajSeqNewNameS (
      const AjPStr str,
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr str Input Sequence string

const AjPStr name Input Sequence name

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
const AjPStr	str	Input	Sequence string
const AjPStr	name	Input	Sequence name
AjPSeq		RETURN	New sequence object.

Input

str:	(Input)	Sequence string
name:	(Input)	Sequence name

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object with a specified existing sequence as a string

Availability

In release 6.4.0

Function ajSeqNewRangeC

Creates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.

The sequence is set to be already trimmed and if necessary reversed.

Start and end positions are 0 (full sequence), as it is trimmed. Any start and end are represented by the offsets.

Synopsis

Prototype

AjPSeq ajSeqNewRangeC (
      const char* txt,
      ajint offset,
      ajint offend,
      AjBool rev
);

Type Name Read/Write Description

const char* txt Input Sequence string

ajint offset Input Offset at start

ajint offend Input Offset at end

AjBool rev Input Reversed if true (reverses offsets)

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
const char*	txt	Input	Sequence string
ajint	offset	Input	Offset at start
ajint	offend	Input	Offset at end
AjBool	rev	Input	Reversed if true (reverses offsets)
AjPSeq		RETURN	New sequence object.

Input

txt:	(Input)	Sequence string
offset:	(Input)	Offset at start
offend:	(Input)	Offset at end
rev:	(Input)	Reversed if true (reverses offsets)

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.

The sequence is set to be already trimmed and if necessary reversed.

Start and end positions are 0 (full sequence), as it is trimmed. Any start and end are represented by the offsets.

Availability

In release 6.4.0

Function ajSeqNewRangeS

Creates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.

The sequence is set to be already trimmed and if necessary reversed.

Start and end positions are 0 (full sequence), as it is trimmed. Any start and end are represented by the offsets.

Synopsis

Prototype

AjPSeq ajSeqNewRangeS (
      const AjPStr str,
      ajint offset,
      ajint offend,
      AjBool rev
);

Type Name Read/Write Description

const AjPStr str Input Sequence string

ajint offset Input Offset at start

ajint offend Input Offset at end

AjBool rev Input Reversed if true (reverses offsets)

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
const AjPStr	str	Input	Sequence string
ajint	offset	Input	Offset at start
ajint	offend	Input	Offset at end
AjBool	rev	Input	Reversed if true (reverses offsets)
AjPSeq		RETURN	New sequence object.

Input

str:	(Input)	Sequence string
offset:	(Input)	Offset at start
offend:	(Input)	Offset at end
rev:	(Input)	Reversed if true (reverses offsets)

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.

The sequence is set to be already trimmed and if necessary reversed.

Start and end positions are 0 (full sequence), as it is trimmed. Any start and end are represented by the offsets.

Availability

In release 6.4.0

Function ajSeqNewRes

Creates and initialises a sequence object with a specified sequence length.

Synopsis

Prototype

AjPSeq ajSeqNewRes (
      size_t size
);

Type Name Read/Write Description

size_t size Input Reserved space for the sequence, including a trailing null character.

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
size_t	size	Input	Reserved space for the sequence, including a trailing null character.
AjPSeq		RETURN	New sequence object.

Input

size:

(Input)

Reserved space for the sequence, including a trailing null character.

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object with a specified sequence length.

Availability

In release 6.4.0

Function ajSeqNewSeq

Creates and initialises a sequence object with a specified existing sequence.

Synopsis

Prototype

AjPSeq ajSeqNewSeq (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Old sequence object

AjPSeq RETURN New sequence object.

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Old sequence object
AjPSeq		RETURN	New sequence object.

Input

seq:

(Input)

Old sequence object

Returns

AjPSeq:

New sequence object.

Description

Creates and initialises a sequence object with a specified existing sequence.

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions: ajSeqDel ajSeqDelarray

Function ajSeqDel

Deletes a sequence object.

Synopsis

Prototype

void ajSeqDel (
      AjPSeq* Pseq
);

Type Name Read/Write Description

AjPSeq* Pseq Delete Sequence object

void RETURN

Type	Name	Read/Write	Description
AjPSeq*	Pseq	Delete	Sequence object
void		RETURN

Output

Pseq:

(Delete)

Sequence object

Returns

void:

No return value

Description

Deletes a sequence object.

Availability

In release 6.4.0

Function ajSeqDelarray

Destructor for array of sequence objects

Synopsis

Prototype

void ajSeqDelarray (
      AjPSeq** PPseq
);

Type Name Read/Write Description

AjPSeq** PPseq Delete Sequence object array

void RETURN

Type	Name	Read/Write	Description
AjPSeq**	PPseq	Delete	Sequence object array
void		RETURN

Output

PPseq:

(Delete)

Sequence object array

Returns

void:

No return value

Description

Destructor for array of sequence objects

Availability

In release 6.4.0

Section: modifiers

These functions update contents of a sequence object.

Functions: ajSeqAddCmt ajSeqAddGene ajSeqAddKey ajSeqAddRef ajSeqAddXref ajSeqAssignAccC ajSeqAssignAccS ajSeqAssignDescC ajSeqAssignDescS ajSeqAssignEntryC ajSeqAssignEntryS ajSeqAssignFileC ajSeqAssignFileS ajSeqAssignFullC ajSeqAssignFullS ajSeqAssignGiC ajSeqAssignGiS ajSeqAssignNameC ajSeqAssignNameS ajSeqAssignQualLen ajSeqAssignSeqC ajSeqAssignSeqLenC ajSeqAssignSeqS ajSeqAssignSvC ajSeqAssignSvS ajSeqAssignUfoC ajSeqAssignUfoS ajSeqAssignUsaC ajSeqAssignUsaS ajSeqClear ajSeqSetName ajSeqSetNameMulti ajSeqSetOffsets ajSeqSetRange ajSeqSetRangeRev ajSeqSetUnique ajSeqTagRev

Function ajSeqAddCmt

Adds a comment to a sequence object

Synopsis

Prototype

void ajSeqAddCmt (
      AjPSeq seq,
      AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

AjPStr str Modify Comment.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
AjPStr	str	Modify	Comment.
void		RETURN

Input & Output

seq:	(Modify)	Sequence object.
str:	(Modify)	Comment.

Returns

void:

No return value

Description

Adds a comment to a sequence object

Availability

In release 6.4.0

Function ajSeqAddGene

Adds a gene to a sequence object

Synopsis

Prototype

void ajSeqAddGene (
      AjPSeq seq,
      AjPSeqGene gene
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

AjPSeqGene gene Modify Gene object

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
AjPSeqGene	gene	Modify	Gene object
void		RETURN

Input & Output

seq:	(Modify)	Sequence object.
gene:	(Modify)	Gene object

Returns

void:

No return value

Description

Adds a gene to a sequence object

Availability

In release 6.4.0

Function ajSeqAddKey

Adds a keyword to a sequence object

Synopsis

Prototype

void ajSeqAddKey (
      AjPSeq seq,
      AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

AjPStr str Modify Comment.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
AjPStr	str	Modify	Comment.
void		RETURN

Input & Output

seq:	(Modify)	Sequence object.
str:	(Modify)	Comment.

Returns

void:

No return value

Description

Adds a keyword to a sequence object

Availability

In release 6.4.0

Function ajSeqAddRef

Adds a literature reference to a sequence object

Synopsis

Prototype

void ajSeqAddRef (
      AjPSeq seq,
      AjPSeqRef ref
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

AjPSeqRef ref Modify Literature reference.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
AjPSeqRef	ref	Modify	Literature reference.
void		RETURN

Input & Output

seq:	(Modify)	Sequence object.
ref:	(Modify)	Literature reference.

Returns

void:

No return value

Description

Adds a literature reference to a sequence object

Availability

In release 6.4.0

Function ajSeqAddXref

Adds a cross-reference to a sequence object

Synopsis

Prototype

void ajSeqAddXref (
      AjPSeq seq,
      AjPSeqXref xref
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

AjPSeqXref xref Modify Comment.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
AjPSeqXref	xref	Modify	Comment.
void		RETURN

Input & Output

seq:	(Modify)	Sequence object.
xref:	(Modify)	Comment.

Returns

void:

No return value

Description

Adds a cross-reference to a sequence object

Availability

In release 6.4.0

Function ajSeqAssignAccC

Assigns the sequence accession number.

Synopsis

Prototype

void ajSeqAssignAccC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input Accession number as a C character string.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
const char*	txt	Input	Accession number as a C character string.
void		RETURN

Input

txt:

(Input)

Accession number as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence accession number.

Availability

In release 6.4.0

Function ajSeqAssignAccS

Assigns the sequence accession number.

Synopsis

Prototype

void ajSeqAssignAccS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input Accession number as a string.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
const AjPStr	str	Input	Accession number as a string.
void		RETURN

Input

str:

(Input)

Accession number as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence accession number.

Availability

In release 6.4.0

Function ajSeqAssignDescC

Assigns a modified description to an existing AjPSeq sequence.

Synopsis

Prototype

void ajSeqAssignDescC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input New description as a C character string.

void RETURN

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
const char*	txt	Input	New description as a C character string.
void		RETURN

Input

txt:

(Input)

New description as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns a modified description to an existing AjPSeq sequence.

Availability

In release 6.4.0

Function ajSeqAssignDescS

Assigns a modified description to an existing AjPSeq sequence.

Synopsis

Prototype

void ajSeqAssignDescS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input New description as a string.

void RETURN

Input

str:

(Input)

New description as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns a modified description to an existing AjPSeq sequence.

Availability

In release 6.4.0

Function ajSeqAssignEntryC

Assigns the sequence entryname.

Synopsis

Prototype

void ajSeqAssignEntryC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input Entry name as a C character string.

void RETURN

Input

txt:

(Input)

Entry name as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence entryname.

Availability

In release 6.4.0

Function ajSeqAssignEntryS

Assigns the sequence entryname.

Synopsis

Prototype

void ajSeqAssignEntryS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input Entry name as a string.

void RETURN

Input

str:

(Input)

Entry name as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence entryname.

Availability

In release 6.4.0

Function ajSeqAssignFileC

Assigns the sequence filename.

Synopsis

Prototype

void ajSeqAssignFileC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input File name as a C character string.

void RETURN

Input

txt:

(Input)

File name as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence filename.

Availability

In release 6.4.0

Function ajSeqAssignFileS

Assigns the sequence file name.

Synopsis

Prototype

void ajSeqAssignFileS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input File name as a string.

void RETURN

Input

str:

(Input)

File name as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence file name.

Availability

In release 6.4.0

Function ajSeqAssignFullC

Assigns the sequence name.

Synopsis

Prototype

void ajSeqAssignFullC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input Full name as a C character string.

void RETURN

Input

txt:

(Input)

Full name as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence name.

Availability

In release 6.4.0

Function ajSeqAssignFullS

Assigns the sequence full name.

Synopsis

Prototype

void ajSeqAssignFullS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input Full name as a string.

void RETURN

Input

str:

(Input)

Full name as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence full name.

Availability

In release 6.4.0

Function ajSeqAssignGiC

Assigns the GI version number.

Synopsis

Prototype

void ajSeqAssignGiC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input GI number as a C character string.

void RETURN

Input

txt:

(Input)

GI number as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the GI version number.

Availability

In release 6.4.0

Function ajSeqAssignGiS

Assigns the GI version number.

Synopsis

Prototype

void ajSeqAssignGiS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input GI number as a string.

void RETURN

Input

str:

(Input)

GI number as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the GI version number.

Availability

In release 6.4.0

Function ajSeqAssignNameC

Assigns the sequence name.

Synopsis

Prototype

void ajSeqAssignNameC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input Name as a string.

void RETURN

Input

txt:

(Input)

Name as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence name.

Availability

In release 6.4.0

Function ajSeqAssignNameS

Assigns the sequence name.

Synopsis

Prototype

void ajSeqAssignNameS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input Name as a string.

void RETURN

Input

str:

(Input)

Name as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence name.

Availability

In release 6.4.0

Function ajSeqAssignQualLen

Assigns base quality scores to an existing sequence.

Synopsis

Prototype

void ajSeqAssignQualLen (
      AjPSeq seq,
      const float* qual,
      ajuint len
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const float* qual Input Base quality scores.

ajuint len Input Number of quality scores to use

void RETURN

Input

qual:	(Input)	Base quality scores.
len:	(Input)	Number of quality scores to use

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns base quality scores to an existing sequence.

Availability

In release 6.4.0

Function ajSeqAssignSeqC

Assigns a modified sequence to an existing AjPSeq sequence.

Synopsis

Prototype

void ajSeqAssignSeqC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input New sequence as a C character string.

void RETURN

Input

txt:

(Input)

New sequence as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns a modified sequence to an existing AjPSeq sequence.

Availability

In release 6.4.0

Function ajSeqAssignSeqLenC

Assigns a modified sequence to an existing AjPSeq sequence.

Synopsis

Prototype

void ajSeqAssignSeqLenC (
      AjPSeq seq,
      const char* txt,
      ajuint len
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input New sequence as a C character string.

ajuint len Input Number of characters to use

void RETURN

Input

txt:	(Input)	New sequence as a C character string.
len:	(Input)	Number of characters to use

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns a modified sequence to an existing AjPSeq sequence.

Availability

In release 6.4.0

Function ajSeqAssignSeqS

Assigns a modified sequence to an existing AjPSeq sequence.

Synopsis

Prototype

void ajSeqAssignSeqS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input New sequence as a string.

void RETURN

Input

str:

(Input)

New sequence as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns a modified sequence to an existing AjPSeq sequence.

Availability

In release 6.4.0

Function ajSeqAssignSvC

Assigns the sequence version number.

Synopsis

Prototype

void ajSeqAssignSvC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input SeqVersion number as a C character string.

void RETURN

Input

txt:

(Input)

SeqVersion number as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence version number.

Availability

In release 6.4.0

Function ajSeqAssignSvS

Assigns the sequence version number.

Synopsis

Prototype

void ajSeqAssignSvS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input SeqVersion number as a string.

void RETURN

Input

str:

(Input)

SeqVersion number as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence version number.

Availability

In release 6.4.0

Function ajSeqAssignUfoC

Assigns the sequence feature file name.

Synopsis

Prototype

void ajSeqAssignUfoC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input UFO as a C character string.

void RETURN

Input

txt:

(Input)

UFO as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence feature file name.

Availability

In release 6.4.0

Function ajSeqAssignUfoS

Assigns the sequence feature file name.

Synopsis

Prototype

void ajSeqAssignUfoS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input UFO as a string.

void RETURN

Input

str:

(Input)

UFO as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence feature file name.

Availability

In release 6.4.0

Function ajSeqAssignUsaC

Assigns the sequence full name.

Synopsis

Prototype

void ajSeqAssignUsaC (
      AjPSeq seq,
      const char* txt
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const char* txt Input USA as a C character string.

void RETURN

Input

txt:

(Input)

USA as a C character string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence full name.

Availability

In release 6.4.0

Function ajSeqAssignUsaS

Assigns the sequence full name.

Synopsis

Prototype

void ajSeqAssignUsaS (
      AjPSeq seq,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object.

const AjPStr str Input USA as a string.

void RETURN

Input

str:

(Input)

USA as a string.

Input & Output

seq:

(Modify)

Sequence object.

Returns

void:

No return value

Description

Assigns the sequence full name.

Availability

In release 6.4.0

Function ajSeqClear

Resets all data for a sequence object so that it can be reused.

Synopsis

Prototype

void ajSeqClear (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Resets all data for a sequence object so that it can be reused.

Availability

In release 6.4.0

Function ajSeqSetName

Provides a unique (for this program run) name for a sequence.

Synopsis

Prototype

void ajSeqSetName (
      AjPSeq seq,
      const AjPStr setname
);

Type Name Read/Write Description

AjPSeq seq Output Sequence object

const AjPStr setname Input Name set by caller

void RETURN

Input

setname:

(Input)

Name set by caller

Output

seq:

(Output)

Sequence object

Returns

void:

No return value

Description

Provides a unique (for this program run) name for a sequence.

Availability

In release 6.4.0

Function ajSeqSetNameMulti

Provides a unique (for this program run) name for a sequence. If a name is generated, append a count

Synopsis

Prototype

void ajSeqSetNameMulti (
      AjPSeq seq,
      const AjPStr setname
);

Type Name Read/Write Description

AjPSeq seq Output Sequence object

const AjPStr setname Input Name set by caller

void RETURN

Input

setname:

(Input)

Name set by caller

Output

seq:

(Output)

Sequence object

Returns

void:

No return value

Description

Provides a unique (for this program run) name for a sequence. If a name is generated, append a count

Availability

In release 6.4.0

Function ajSeqSetOffsets

Sets the offsets for each end of a subsequence.

Needed mainly for local alignments so the original sequence numbering can be preserved.

Synopsis

Prototype

void ajSeqSetOffsets (
      AjPSeq seq,
      ajint offset,
      ajint origlen
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object to be set.

ajint offset Input Offset from start of original sequence

ajint origlen Input Original length, used to calculate the offset from the end.

void RETURN

Input

offset:	(Input)	Offset from start of original sequence
origlen:	(Input)	Original length, used to calculate the offset from the end.

Input & Output

seq:

(Modify)

Sequence object to be set.

Returns

void:

No return value

Description

Sets the offsets for each end of a subsequence.

Needed mainly for local alignments so the original sequence numbering can be preserved.

Availability

In release 6.4.0

Function ajSeqSetRange

Sets the start and end positions for a sequence (not for a sequence set). Trim the sequence to convert to the subsequence.

Synopsis

Prototype

void ajSeqSetRange (
      AjPSeq seq,
      ajint pos1,
      ajint pos2
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object to be set.

ajint pos1 Input Start position. Negative values are from the end.

ajint pos2 Input End position. Negative values are from the end.

void RETURN

Input

pos1:	(Input)	Start position. Negative values are from the end.
pos2:	(Input)	End position. Negative values are from the end.

Input & Output

seq:

(Modify)

Sequence object to be set.

Returns

void:

No return value

Description

Sets the start and end positions for a sequence (not for a sequence set). Trim the sequence to convert to the subsequence.

Availability

In release 6.4.0

Function ajSeqSetRangeRev

Sets the start and end positions for a sequence (not for a sequence set), and set the sequence to be reversed.

Synopsis

Prototype

void ajSeqSetRangeRev (
      AjPSeq seq,
      ajint pos1,
      ajint pos2
);

Input

pos1:	(Input)	Start position. Negative values are from the end.
pos2:	(Input)	End position. Negative values are from the end.

Input & Output

seq:

(Modify)

Sequence object to be set.

Returns

void:

No return value

Description

Sets the start and end positions for a sequence (not for a sequence set), and set the sequence to be reversed.

Availability

In release 6.4.0

Function ajSeqSetUnique

Makes a sequence modifiable by making sure there is no duplicate copy of the sequence.

Synopsis

Prototype

void ajSeqSetUnique (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Makes a sequence modifiable by making sure there is no duplicate copy of the sequence.

Availability

In release 6.4.0

Function ajSeqTagRev

Adds a tag to the sequence description to note it has been reversed

Synopsis

Prototype

void ajSeqTagRev (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object to be set.

void RETURN

Input & Output

seq:

(Modify)

Sequence object to be set.

Returns

void:

No return value

Description

Adds a tag to the sequence description to note it has been reversed

Availability

In release 6.4.0

Section: process

These functions use the contents of a sequence object to produce a subsequence from the range, or to reverse a sequence whose direction has been set to be reversed.

Functions: ajSeqComplement ajSeqFmtLower ajSeqFmtUpper ajSeqGapFill ajSeqGapStandard ajSeqReverseDo ajSeqReverseForce ajSeqReverseOnly ajSeqTrim

Function ajSeqComplement

Complements but does not reverse a nucleotide sequence.

Synopsis

Prototype

void ajSeqComplement (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Complements but does not reverse a nucleotide sequence.

Availability

In release 6.4.0

Function ajSeqFmtLower

Converts a sequence to lower case.

Synopsis

Prototype

void ajSeqFmtLower (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Converts a sequence to lower case.

Availability

In release 6.4.0

Function ajSeqFmtUpper

Converts a sequence to upper case.

Synopsis

Prototype

void ajSeqFmtUpper (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Converts a sequence to upper case.

Availability

In release 6.4.0

Function ajSeqGapFill

Fills a single sequence with gaps up to a specified length.

Synopsis

Prototype

void ajSeqGapFill (
      AjPSeq seq,
      ajuint len
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence object to be set.

ajuint len Input Length to pad fill to.

void RETURN

Input

len:

(Input)

Length to pad fill to.

Input & Output

seq:

(Modify)

Sequence object to be set.

Returns

void:

No return value

Description

Fills a single sequence with gaps up to a specified length.

Availability

In release 6.4.0

Function ajSeqGapStandard

Makes all gaps in a string use a standard gap character

Synopsis

Prototype

void ajSeqGapStandard (
      AjPSeq seq,
      char gapchar
);

Type Name Read/Write Description

AjPSeq seq Output Sequence object

char gapchar Input Gap character (or '-' if zero)

void RETURN

Input

gapchar:

(Input)

Gap character (or '-' if zero)

Output

seq:

(Output)

Sequence object

Returns

void:

No return value

Description

Makes all gaps in a string use a standard gap character

Availability

In release 6.4.0

Function ajSeqReverseDo

Reverses and complements a nucleotide sequence, unless it is already done.

If the sequence is not flagged for reversal, use ajSeqReverseForce instead.

Synopsis

Prototype

void ajSeqReverseDo (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Reverses and complements a nucleotide sequence, unless it is already done.

If the sequence is not flagged for reversal, use ajSeqReverseForce instead.

Availability

In release 6.4.0

Function ajSeqReverseForce

Reverses and complements a nucleotide sequence. Forces reversal to be done even if the sequence is flagged as already reversed.

This happens, for example, where an input sequence has been reversed with -sreverse on the command line, but the application needs to reverse it in processing both directions.

Synopsis

Prototype

void ajSeqReverseForce (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Reverses and complements a nucleotide sequence. Forces reversal to be done even if the sequence is flagged as already reversed.

This happens, for example, where an input sequence has been reversed with -sreverse on the command line, but the application needs to reverse it in processing both directions.

Availability

In release 6.4.0

Function ajSeqReverseOnly

Reverses but does not complement a nucleotide sequence.

Intended for sequence display, but can be used to fix incorrect sequence entries.

Synopsis

Prototype

void ajSeqReverseOnly (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence

void RETURN

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

Reverses but does not complement a nucleotide sequence.

Intended for sequence display, but can be used to fix incorrect sequence entries.

Availability

In release 6.4.0

Function ajSeqTrim

Trim a sequence using the Begin and Ends. Also reverse complements a nucleotide sequence if required.

Synopsis

Prototype

void ajSeqTrim (
      AjPSeq seq
);

Type Name Read/Write Description

AjPSeq seq Modify Sequence to be trimmed.

void RETURN

Input & Output

seq:

(Modify)

Sequence to be trimmed.

Returns

void:

No return value

Description

Trim a sequence using the Begin and Ends. Also reverse complements a nucleotide sequence if required.

Availability

In release 6.4.0

Section: element retrieval

These functions return the contents of a sequence object.

Functions: ajSeqGetAccC ajSeqGetAccS ajSeqGetBegin ajSeqGetBeginTrue ajSeqGetDbC ajSeqGetDbS ajSeqGetDescC ajSeqGetDescS ajSeqGetEnd ajSeqGetEndTrue ajSeqGetEntryC ajSeqGetEntryS ajSeqGetFeat ajSeqGetFeatCopy ajSeqGetGiC ajSeqGetGiS ajSeqGetLen ajSeqGetLenTrimmed ajSeqGetLenTrue ajSeqGetLenUngapped ajSeqGetNameC ajSeqGetNameS ajSeqGetOffend ajSeqGetOffset ajSeqGetQual ajSeqGetRange ajSeqGetRev ajSeqGetSeqC ajSeqGetSeqS ajSeqGetSeqCopyC ajSeqGetSeqCopyS ajSeqGetSvC ajSeqGetSvS ajSeqGetTaxC ajSeqGetTaxS ajSeqGetTaxid ajSeqGetUsaC ajSeqGetUsaS ajSeqGetXrefs

Function ajSeqGetAccC

Returns the sequence accession number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetAccC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN Accession number as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

Accession number as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetAccS

Synopsis

Prototype

const AjPStr ajSeqGetAccS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN Accession number as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Accession number as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetBegin

Returns the sequence start position within the current stored sequence, or 1 if no start has been set.

To return the position within the original sequence, which may be different if the sequence has been trimmed, use ajSeqGetBeginTrue

Synopsis

Prototype

ajuint ajSeqGetBegin (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Start position.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Start position.

Description

Returns the sequence start position within the current stored sequence, or 1 if no start has been set.

To return the position within the original sequence, which may be different if the sequence has been trimmed, use ajSeqGetBeginTrue

Availability

In release 6.4.0

Function ajSeqGetBeginTrue

Returns the sequence start position in the original sequence, which may have been trimmed.

To return the position within the current stored sequence, which may be different if the sequence has been trimmed, use ajSeqBegin

Synopsis

Prototype

ajuint ajSeqGetBeginTrue (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Start position.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Start position.

Description

Returns the sequence start position in the original sequence, which may have been trimmed.

To return the position within the current stored sequence, which may be different if the sequence has been trimmed, use ajSeqBegin

Availability

In release 6.4.0

Function ajSeqGetDbC

Returns the sequence database name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetDbC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN Database name as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

Database name as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetDbS

Synopsis

Prototype

const AjPStr ajSeqGetDbS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN Database name as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Database name as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetDescC

Returns the sequence description. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetDescC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN Description as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

Description as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetDescS

Synopsis

Prototype

const AjPStr ajSeqGetDescS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN Description as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Description as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetEnd

Returns the sequence end position, or the sequence length if no end has been set.

Synopsis

Prototype

ajuint ajSeqGetEnd (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN End position.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

End position.

Description

Returns the sequence end position, or the sequence length if no end has been set.

Availability

In release 6.4.0

Function ajSeqGetEndTrue

Returns the sequence end position, or the sequence length if no end has been set.

Synopsis

Prototype

ajuint ajSeqGetEndTrue (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN End position.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

End position.

Description

Returns the sequence end position, or the sequence length if no end has been set.

Availability

In release 6.4.0

Function ajSeqGetEntryC

Returns the sequence full text entry. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetEntryC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN Entry as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

Entry as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetEntryS

Synopsis

Prototype

const AjPStr ajSeqGetEntryS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN Entry as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Entry as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetFeat

Returns the sequence feature table. Because this is a pointer to the real internal table the caller must take care not to change it in any way, or to delete it.

If the table is to be changed or deleted then it must first be copied with ajSeqCopyFeat

Synopsis

Prototype

const AjPFeattable ajSeqGetFeat (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPFeattable RETURN feature table (if any)

Input

seq:

(Input)

Sequence object.

Returns

const AjPFeattable:

feature table (if any)

Description

Returns the sequence feature table. Because this is a pointer to the real internal table the caller must take care not to change it in any way, or to delete it.

If the table is to be changed or deleted then it must first be copied with ajSeqCopyFeat

Availability

In release 6.4.0

Function ajSeqGetFeatCopy

Returns a copy of the sequence feature table. Because this is a copy of all the data, the caller is responsible for deleting it after use.

If the table is not to be changed or deleted then ajSeqGetFeat can return a copy of the internal pointer.

Synopsis

Prototype

AjPFeattable ajSeqGetFeatCopy (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

AjPFeattable RETURN feature table (if any)

Input

seq:

(Input)

Sequence object.

Returns

AjPFeattable:

feature table (if any)

Description

Returns a copy of the sequence feature table. Because this is a copy of all the data, the caller is responsible for deleting it after use.

If the table is not to be changed or deleted then ajSeqGetFeat can return a copy of the internal pointer.

Availability

In release 6.4.0

Function ajSeqGetGiC

Returns the GI version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetGiC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN SeqVersion number as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

SeqVersion number as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetGiS

Synopsis

Prototype

const AjPStr ajSeqGetGiS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN SeqVersion number as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

SeqVersion number as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetLen

Returns the sequence length.

Synopsis

Prototype

ajuint ajSeqGetLen (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Sequence length.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Sequence length.

Description

Returns the sequence length.

Availability

In release 6.4.0

Function ajSeqGetLenTrimmed

Returns the sequence length after trimming begin and end positions

Synopsis

Prototype

ajuint ajSeqGetLenTrimmed (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Sequence length.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Sequence length.

Description

Returns the sequence length after trimming begin and end positions

Availability

In release 6.4.0

Function ajSeqGetLenTrue

Returns the length of the original sequence, including any gap characters.

Synopsis

Prototype

ajuint ajSeqGetLenTrue (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Target sequence.

ajuint RETURN string position between 1 and length.

Input

seq:

(Input)

Target sequence.

Returns

ajuint:

string position between 1 and length.

Description

Returns the length of the original sequence, including any gap characters.

Availability

In release 6.4.0

Function ajSeqGetLenUngapped

Returns the sequence length excluding all gap characters.

Synopsis

Prototype

ajuint ajSeqGetLenUngapped (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Sequence length.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Sequence length.

Description

Returns the sequence length excluding all gap characters.

Availability

In release 6.4.0

Function ajSeqGetNameC

Returns the sequence name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetNameC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN Name as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

Name as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetNameS

Synopsis

Prototype

const AjPStr ajSeqGetNameS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetOffend

Returns the sequence offend value. This is the number of positions removed from the original end.

Synopsis

Prototype

ajuint ajSeqGetOffend (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Sequence offend.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Sequence offend.

Description

Returns the sequence offend value. This is the number of positions removed from the original end.

Availability

In release 6.4.0

Function ajSeqGetOffset

Returns the sequence offset from -sbegin originally.

Synopsis

Prototype

ajuint ajSeqGetOffset (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Sequence offset.

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Sequence offset.

Description

Returns the sequence offset from -sbegin originally.

Availability

In release 6.4.0

Function ajSeqGetQual

Returns the base quality scores as an array. Because this is a pointer to the real internal array the caller must take care not to change the array in any way.

Synopsis

Prototype

const float* ajSeqGetQual (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence.

const float* RETURN Base quality scores.

Input

seq:

(Input)

Sequence.

Returns

const float*:

Base quality scores.

Description

Returns the base quality scores as an array. Because this is a pointer to the real internal array the caller must take care not to change the array in any way.

Availability

In release 6.4.0

Function ajSeqGetRange

Returns the sequence range for a sequence.

Synopsis

Prototype

ajuint ajSeqGetRange (
      const AjPSeq seq,
      ajint* begin,
      ajint* end
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

ajint* begin Output Sequence range begin

ajint* end Output Sequence range end

ajuint RETURN Sequence range length

Input

seq:

(Input)

Sequence object.

Output

begin:	(Output)	Sequence range begin
end:	(Output)	Sequence range end

Returns

ajuint:

Sequence range length

Description

Returns the sequence range for a sequence.

Availability

In release 6.4.0

Function ajSeqGetRev

Returns the sequence direction.

See ajSeqReversed for whether it has already been reverse-complemented

Synopsis

Prototype

AjBool ajSeqGetRev (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

AjBool RETURN Sequence Direction.

Input

seq:

(Input)

Sequence object

Returns

AjBool:

Sequence Direction.

Description

Returns the sequence direction.

See ajSeqReversed for whether it has already been reverse-complemented

Availability

In release 6.4.0

Function ajSeqGetSeqC

Returns the sequence in a sequence object as a character string. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetSeqC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence.

const char* RETURN Sequence as a character string.

Input

seq:

(Input)

Sequence.

Returns

const char*:

Sequence as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetSeqS

Returns the sequence in a sequence object as a string. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const AjPStr ajSeqGetSeqS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence.

const AjPStr RETURN Sequence as a string.

Input

seq:

(Input)

Sequence.

Returns

const AjPStr:

Sequence as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetSeqCopyC

Returns a sequence as a C character string. This is a copy of the string so the caller can do anything with it. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.

Synopsis

Prototype

char* ajSeqGetSeqCopyC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

char* RETURN Sequence as a null terminated character string.

Input

seq:

(Input)

Sequence object

Returns

char*:

Sequence as a null terminated character string.

Description

Returns a sequence as a C character string. This is a copy of the string so the caller can do anything with it. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.

Availability

In release 6.4.0

Function ajSeqGetSeqCopyS

Returns the sequence in a sequence object as a string. Because this is a copy of the internal string the caller may change the string. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.

Synopsis

Prototype

AjPStr ajSeqGetSeqCopyS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence.

AjPStr RETURN Sequence as a string.

Input

seq:

(Input)

Sequence.

Returns

AjPStr:

Sequence as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetSvC

Returns the sequence version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetSvC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN SeqVersion number as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

SeqVersion number as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetSvS

Synopsis

Prototype

const AjPStr ajSeqGetSvS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN SeqVersion number as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

SeqVersion number as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetTaxC

Returns the sequence primary taxon (species). Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetTaxC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN Description as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

Description as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetTaxS

Synopsis

Prototype

const AjPStr ajSeqGetTaxS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN Description as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Description as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetTaxid

Returns the numeric identifier of the sequence primary taxon (species). This is an identifier from the NCBI taxonomy

Synopsis

Prototype

ajuint ajSeqGetTaxid (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

ajuint RETURN Taxon ID.

Input

seq:

(Input)

Sequence object.

Returns

ajuint:

Taxon ID.

Description

Returns the numeric identifier of the sequence primary taxon (species). This is an identifier from the NCBI taxonomy

Availability

In release 6.4.0

Function ajSeqGetUsaC

Returns the original USA of a sequence. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const char* ajSeqGetUsaC (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const char* RETURN USA as a character string.

Input

seq:

(Input)

Sequence object.

Returns

const char*:

USA as a character string.

Description

Availability

In release 6.4.0

Function ajSeqGetUsaS

Synopsis

Prototype

const AjPStr ajSeqGetUsaS (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

const AjPStr RETURN USA as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

USA as a string.

Description

Availability

In release 6.4.0

Function ajSeqGetXrefs

Returns the list of cross-references derived from the sequence

Synopsis

Prototype

ajuint ajSeqGetXrefs (
      const AjPSeq seq,
      AjPList list
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object.

AjPList list Modify List of cross-reference objects

ajuint RETURN NUmber of cross-references returned

Input

seq:

(Input)

Sequence object.

Input & Output

list:

(Modify)

List of cross-reference objects

Returns

ajuint:

NUmber of cross-references returned

Description

Returns the list of cross-references derived from the sequence

Availability

In release 6.4.0

Section: testing properties

Functions: ajSeqIsNuc ajSeqIsProt ajSeqIsReversed ajSeqIsReversedTrue ajSeqIsSpeciesBsubtilis ajSeqIsSpeciesHuman ajSeqIsSpeciesMouse ajSeqIsSpeciesYeast ajSeqIsTaxon ajSeqIsTrimmed

Function ajSeqIsNuc

Tests whether a sequence is nucleotide.

Synopsis

Prototype

AjBool ajSeqIsNuc (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

AjBool RETURN ajTrue for a nucleotide sequence.

Input

seq:

(Input)

Sequence

Returns

AjBool:

ajTrue for a nucleotide sequence.

Description

Tests whether a sequence is nucleotide.

Availability

In release 6.4.0

Function ajSeqIsProt

Tests whether a sequence is protein.

Synopsis

Prototype

AjBool ajSeqIsProt (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

AjBool RETURN ajTrue for a protein sequence.

Input

seq:

(Input)

Sequence

Returns

AjBool:

ajTrue for a protein sequence.

Description

Tests whether a sequence is protein.

Availability

In release 6.4.0

Function ajSeqIsReversed

Returns whether the sequence has been reversed

Synopsis

Prototype

AjBool ajSeqIsReversed (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

AjBool RETURN Sequence Direction.

Input

seq:

(Input)

Sequence object

Returns

AjBool:

Sequence Direction.

Description

Returns whether the sequence has been reversed

Availability

In release 6.4.0

Function ajSeqIsReversedTrue

Returns ajTrue if the sequence is reversed relative to the original sequence

If the sequence has already been reversed, or is set to be reversed, the result will be true.

Synopsis

Prototype

AjBool ajSeqIsReversedTrue (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

AjBool RETURN ajTrue if sequence is set to be reversed

Input

seq:

(Input)

Sequence object

Returns

AjBool:

ajTrue if sequence is set to be reversed

Description

Returns ajTrue if the sequence is reversed relative to the original sequence

If the sequence has already been reversed, or is set to be reversed, the result will be true.

Availability

In release 6.4.0

Function ajSeqIsSpeciesBsubtilis

Tests whether a sequence is annotated as B. subtilis

Synopsis

Prototype

AjBool ajSeqIsSpeciesBsubtilis (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

AjBool RETURN ajTrue for a nucleotide sequence.

Input

seq:

(Input)

Sequence

Returns

AjBool:

ajTrue for a nucleotide sequence.

Description

Tests whether a sequence is annotated as B. subtilis

Availability

In release 6.4.0

Function ajSeqIsSpeciesHuman

Tests whether a sequence is annotated as human

Synopsis

Prototype

AjBool ajSeqIsSpeciesHuman (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

AjBool RETURN ajTrue for a nucleotide sequence.

Input

seq:

(Input)

Sequence

Returns

AjBool:

ajTrue for a nucleotide sequence.

Description

Tests whether a sequence is annotated as human

Availability

In release 6.4.0

Function ajSeqIsSpeciesMouse

Tests whether a sequence is annotated as mouse

Synopsis

Prototype

AjBool ajSeqIsSpeciesMouse (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

AjBool RETURN ajTrue for a nucleotide sequence.

Input

seq:

(Input)

Sequence

Returns

AjBool:

ajTrue for a nucleotide sequence.

Description

Tests whether a sequence is annotated as mouse

Availability

In release 6.4.0

Function ajSeqIsSpeciesYeast

Tests whether a sequence is annotated as yeast (S. cerevisiae)

Synopsis

Prototype

AjBool ajSeqIsSpeciesYeast (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

AjBool RETURN ajTrue for a nucleotide sequence.

Input

seq:

(Input)

Sequence

Returns

AjBool:

ajTrue for a nucleotide sequence.

Description

Tests whether a sequence is annotated as yeast (S. cerevisiae)

Availability

In release 6.4.0

Function ajSeqIsTaxon

Tests whether a sequence is annotated as from a specific taxon ID.

Synopsis

Prototype

AjBool ajSeqIsTaxon (
      const AjPSeq seq,
      ajuint taxid
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

ajuint taxid Input NCBI Taxonomy ID

AjBool RETURN ajTrue for a nucleotide sequence.

Input

seq:	(Input)	Sequence
taxid:	(Input)	NCBI Taxonomy ID

Returns

AjBool:

ajTrue for a nucleotide sequence.

Description

Tests whether a sequence is annotated as from a specific taxon ID.

Availability

In release 6.4.0

Function ajSeqIsTrimmed

Returns ajTrue if the sequence is already trimmed

Synopsis

Prototype

AjBool ajSeqIsTrimmed (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

AjBool RETURN ajTrue if sequence is set to be reversed

Input

seq:

(Input)

Sequence object

Returns

AjBool:

ajTrue if sequence is set to be reversed

Description

Returns ajTrue if the sequence is already trimmed

Availability

In release 6.4.0

Section: conversion

Convert sequence to numbers for efficient processing

Functions: ajSeqConvertNum

Function ajSeqConvertNum

Converts a string of sequence characters to numbers using a conversion table.

Synopsis

Prototype

AjBool ajSeqConvertNum (
      const AjPSeq seq,
      const AjPSeqCvt cvt,
      AjPStr* Pnumseq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence as a string

const AjPSeqCvt cvt Input Conversion table.

AjPStr* Pnumseq Output Output numeric version of the sequence.

AjBool RETURN ajTrue on success.

Input

seq:	(Input)	Sequence as a string
cvt:	(Input)	Conversion table.

Output

Pnumseq:

(Output)

Output numeric version of the sequence.

Returns

AjBool:

ajTrue on success.

Description

Converts a string of sequence characters to numbers using a conversion table.

Availability

In release 6.4.0

Section: calculated properties

Functions: ajSeqCalcCheckgcg ajSeqCalcCount ajSeqCalcMolwt ajSeqCalcTruepos ajSeqCalcTrueposMin ajSeqCountGaps

Function ajSeqCalcCheckgcg

Calculates a GCG checksum for a sequence.

Synopsis

Prototype

ajint ajSeqCalcCheckgcg (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence.

ajint RETURN GCG checksum.

Input

seq:

(Input)

Sequence.

Returns

ajint:

GCG checksum.

Description

Calculates a GCG checksum for a sequence.

Availability

In release 6.4.0

Function ajSeqCalcCount

Counts the numbers of A, C, G and T in a nucleotide sequence.

Synopsis

Prototype

void ajSeqCalcCount (
      const AjPSeq seq,
      ajint* b
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajint* b Output integer array, minimum size 5, to hold the results.

void RETURN

Input

seq:

(Input)

Sequence object

Output

(Output)

integer array, minimum size 5, to hold the results.

Returns

void:

No return value

Description

Counts the numbers of A, C, G and T in a nucleotide sequence.

Availability

In release 6.4.0

Function ajSeqCalcMolwt

Calculates the molecular weight of a protein sequence.

Synopsis

Prototype

float ajSeqCalcMolwt (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence

float RETURN Molecular weight.

Input

seq:

(Input)

Sequence

Returns

float:

Molecular weight.

Description

Calculates the molecular weight of a protein sequence.

Availability

In release 6.4.0

Function ajSeqCalcTruepos

Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.

For strings, the result can go off the end to the terminating NULL. For sequences the maximum is the last base

Synopsis

Prototype

ajint ajSeqCalcTruepos (
      const AjPSeq seq,
      ajint ipos
);

Type Name Read/Write Description

const AjPSeq seq Input Target sequence.

ajint ipos Input Position.

ajint RETURN string position between 1 and length.

Input

seq:	(Input)	Target sequence.
ipos:	(Input)	Position.

Returns

ajint:

string position between 1 and length.

Description

Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.

For strings, the result can go off the end to the terminating NULL. For sequences the maximum is the last base

Availability

In release 6.4.0

Function ajSeqCalcTrueposMin

Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.

imin is a minimum relative position, also counted from the end if negative. Usually this is the start position when the end of a range is being tested.

Synopsis

Prototype

ajint ajSeqCalcTrueposMin (
      const AjPSeq seq,
      ajint imin,
      ajint ipos
);

Type Name Read/Write Description

const AjPSeq seq Input Target sequence.

ajint imin Input Start position.

ajint ipos Input Position.

ajint RETURN string position between 1 and length.

Input

seq:	(Input)	Target sequence.
imin:	(Input)	Start position.
ipos:	(Input)	Position.

Returns

ajint:

string position between 1 and length.

Description

Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.

imin is a minimum relative position, also counted from the end if negative. Usually this is the start position when the end of a range is being tested.

Availability

In release 6.4.0

Function ajSeqCountGaps

Returns the number of gaps in a sequence (counting any possible gap character

Synopsis

Prototype

ajuint ajSeqCountGaps (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

ajuint RETURN Number of gaps

Input

seq:

(Input)

Sequence object

Returns

ajuint:

Number of gaps

Description

Returns the number of gaps in a sequence (counting any possible gap character

Availability

In release 6.4.0

Section: exit

Functions called on exit from the program by ajExit to do any necessary cleanup and to report internal statistics to the debug file

Functions: ajSeqExit

Function ajSeqExit

Cleans up sequence processing internal memory

Synopsis

Prototype

void ajSeqExit (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Cleans up sequence processing internal memory

Availability

In release 6.4.0

Section: debug

Reports sequence contents for debugging purposes

Functions: ajSeqTrace ajSeqTraceTitle

Function ajSeqTrace

Debug calls to trace the data in a sequence object.

Synopsis

Prototype

void ajSeqTrace (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence.

void RETURN

Input

seq:

(Input)

Sequence.

Returns

void:

No return value

Description

Debug calls to trace the data in a sequence object.

Availability

In release 6.4.0

Function ajSeqTraceTitle

Reports an AjPSeq object to debug output

Synopsis

Prototype

void ajSeqTraceTitle (
      const AjPSeq seq,
      const char* title
);

Type Name Read/Write Description

const AjPSeq seq Input alignment object

const char* title Input Trace report title

void RETURN

Input

seq:	(Input)	alignment object
title:	(Input)	Trace report title

Returns

void:

No return value

Description

Reports an AjPSeq object to debug output

Availability

In release 6.4.0

Datatype: AjPSeqall

Sequence stream

Sections: Sequence Stream Constructors destructors modifiers casts

Section: Sequence Stream Constructors

Functions: ajSeqallNew

Function ajSeqallNew

Creates a new sequence stream object to hold one sequence at a time.

Synopsis

Prototype

AjPSeqall ajSeqallNew (
      void
);

Type Name Read/Write Description

AjPSeqall RETURN New sequence stream object.

Returns

AjPSeqall:

New sequence stream object.

Description

Creates a new sequence stream object to hold one sequence at a time.

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions: ajSeqallDel

Function ajSeqallDel

Destructor for sequence stream objects

Synopsis

Prototype

void ajSeqallDel (
      AjPSeqall* Pseq
);

Type Name Read/Write Description

AjPSeqall* Pseq Delete Sequence stream object reference

void RETURN

Output

Pseq:

(Delete)

Sequence stream object reference

Returns

void:

No return value

Description

Destructor for sequence stream objects

Availability

In release 6.4.0

Section: modifiers

These functions use the contents of a sequence stream object and update them.

Functions: ajSeqallClear ajSeqallClearStats ajSeqallSetRange ajSeqallSetRangeRev

Function ajSeqallClear

Resets all data internals for a sequence stream object when input has been read, but leaves statistics for reporting.

Synopsis

Prototype

void ajSeqallClear (
      AjPSeqall seq
);

Type Name Read/Write Description

AjPSeqall seq Modify Sequence stream

void RETURN

Input & Output

seq:

(Modify)

Sequence stream

Returns

void:

No return value

Description

Resets all data internals for a sequence stream object when input has been read, but leaves statistics for reporting.

Availability

In release 6.4.0

Function ajSeqallClearStats

Resets all data for a sequence stream object so that it can be reused, including statistics.

Synopsis

Prototype

void ajSeqallClearStats (
      AjPSeqall seq
);

Type Name Read/Write Description

AjPSeqall seq Modify Sequence stream

void RETURN

Input & Output

seq:

(Modify)

Sequence stream

Returns

void:

No return value

Description

Resets all data for a sequence stream object so that it can be reused, including statistics.

Availability

In release 6.4.0

Function ajSeqallSetRange

Sets the start and end positions for a sequence stream.

Synopsis

Prototype

void ajSeqallSetRange (
      AjPSeqall seq,
      ajint pos1,
      ajint pos2
);

Type Name Read/Write Description

AjPSeqall seq Modify Sequence stream object to be set.

ajint pos1 Input Start position. Negative values are from the end.

ajint pos2 Input End position. Negative values are from the end.

void RETURN

Input

pos1:	(Input)	Start position. Negative values are from the end.
pos2:	(Input)	End position. Negative values are from the end.

Input & Output

seq:

(Modify)

Sequence stream object to be set.

Returns

void:

No return value

Description

Sets the start and end positions for a sequence stream.

Availability

In release 6.4.0

Function ajSeqallSetRangeRev

Sets the start and end positions for a sequence stream, and set the sequences to be reversed.

Synopsis

Prototype

void ajSeqallSetRangeRev (
      AjPSeqall seq,
      ajint pos1,
      ajint pos2
);

Input

pos1:	(Input)	Start position. Negative values are from the end.
pos2:	(Input)	End position. Negative values are from the end.

Input & Output

seq:

(Modify)

Sequence stream object to be set.

Returns

void:

No return value

Description

Sets the start and end positions for a sequence stream, and set the sequences to be reversed.

Availability

In release 6.4.0

Section: casts

These functions examine the contents of a sequence stream object and return some derived information. Some of them provide access to the internal components of a sequence stream object. They are provided for programming convenience but should be used with caution.

Functions: ajSeqallGetCount ajSeqallGetFilename ajSeqallGetName ajSeqallGetTotlength ajSeqallGetUsa ajSeqallGetseqBegin ajSeqallGetseqEnd ajSeqallGetseqLen ajSeqallGetseqName ajSeqallGetseqRange

Function ajSeqallGetCount

Returns the number of sequences read by a seqall object

Synopsis

Prototype

ajlong ajSeqallGetCount (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Seqall object pointer.

ajlong RETURN Number of sequences read.

Input

seq:

(Input)

Seqall object pointer.

Returns

ajlong:

Number of sequences read.

Description

Returns the number of sequences read by a seqall object

Availability

In release 6.4.0

Function ajSeqallGetFilename

Returns the filename of a seqall object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const AjPStr ajSeqallGetFilename (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Seqall object pointer.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Seqall object pointer.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqallGetName

Returns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const AjPStr ajSeqallGetName (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence stream object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence stream object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqallGetTotlength

Returns the total length of sequences read by a seqall object

Synopsis

Prototype

ajlong ajSeqallGetTotlength (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Seqall object pointer.

ajlong RETURN Total length of sequences read.

Input

seq:

(Input)

Seqall object pointer.

Returns

ajlong:

Total length of sequences read.

Description

Returns the total length of sequences read by a seqall object

Availability

In release 6.4.0

Function ajSeqallGetUsa

Synopsis

Prototype

const AjPStr ajSeqallGetUsa (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqallGetseqBegin

Returns the sequence stream start position, or 1 if no start has been set.

Synopsis

Prototype

ajint ajSeqallGetseqBegin (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence stream object

ajint RETURN Start position.

Input

seq:

(Input)

Sequence stream object

Returns

ajint:

Start position.

Description

Returns the sequence stream start position, or 1 if no start has been set.

Availability

In release 6.4.0

Function ajSeqallGetseqEnd

Returns the sequence stream end position, or the sequence length if no end has been set.

Synopsis

Prototype

ajint ajSeqallGetseqEnd (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence stream object

ajint RETURN Start position.

Input

seq:

(Input)

Sequence stream object

Returns

ajint:

Start position.

Description

Returns the sequence stream end position, or the sequence length if no end has been set.

Availability

In release 6.4.0

Function ajSeqallGetseqLen

Returns the length of a sequence stream, which is the length of the latest sequence read.

Synopsis

Prototype

ajint ajSeqallGetseqLen (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence stream object

ajint RETURN sequence length.

Input

seq:

(Input)

Sequence stream object

Returns

ajint:

sequence length.

Description

Returns the length of a sequence stream, which is the length of the latest sequence read.

Availability

In release 6.4.0

Function ajSeqallGetseqName

Synopsis

Prototype

const AjPStr ajSeqallGetseqName (
      const AjPSeqall seq
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence stream object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence stream object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqallGetseqRange

Returns the sequence range for a sequence stream

Synopsis

Prototype

ajint ajSeqallGetseqRange (
      const AjPSeqall seq,
      ajint* begin,
      ajint* end
);

Type Name Read/Write Description

const AjPSeqall seq Input Sequence stream object.

ajint* begin Output Sequence range begin

ajint* end Output Sequence range end

ajint RETURN Sequence range length

Input

seq:

(Input)

Sequence stream object.

Output

begin:	(Output)	Sequence range begin
end:	(Output)	Sequence range end

Returns

ajint:

Sequence range length

Description

Returns the sequence range for a sequence stream

Availability

In release 6.4.0

Datatype: AjPSeqset

Sequence set

Sections: constructors destructors casts modifiers element assignment casts testing properties

Section: constructors

All constructors return a new sequence set object by pointer. It is the responsibility of the user to first destroy any previous sequence. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions: ajSeqsetNew

Function ajSeqsetNew

Creates a new sequence set object to hold all sequences in memory.

Synopsis

Prototype

AjPSeqset ajSeqsetNew (
      void
);

Type Name Read/Write Description

AjPSeqset RETURN New sequence set object.

Returns

AjPSeqset:

New sequence set object.

Description

Creates a new sequence set object to hold all sequences in memory.

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions: ajSeqsetDel ajSeqsetDelarray

Function ajSeqsetDel

Destructor for sequence set objects

Synopsis

Prototype

void ajSeqsetDel (
      AjPSeqset* Pseq
);

Type Name Read/Write Description

AjPSeqset* Pseq Delete Sequence set object reference

void RETURN

Output

Pseq:

(Delete)

Sequence set object reference

Returns

void:

No return value

Description

Destructor for sequence set objects

Availability

In release 6.4.0

Function ajSeqsetDelarray

Destructor for array of sequence set objects

Synopsis

Prototype

void ajSeqsetDelarray (
      AjPSeqset** PPseq
);

Type Name Read/Write Description

AjPSeqset** PPseq Delete Sequence set object array

void RETURN

Output

PPseq:

(Delete)

Sequence set object array

Returns

void:

No return value

Description

Destructor for array of sequence set objects

Availability

In release 6.4.0

Section: casts

These functions examine the contents of a sequence set object and return some derived information. Some of them provide access to the internal components of a sequence stream object. They are provided for programming convenience but should be used with caution.

Functions: ajSeqsetGetFilename ajSeqsetGetFormat ajSeqsetGetOffend ajSeqsetGetOffset ajSeqsetGetRange ajSeqsetGetTotlength ajSeqsetGetUsa

Function ajSeqsetGetFilename

Returns the filename of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const AjPStr ajSeqsetGetFilename (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence set object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqsetGetFormat

Returns the sequence format for a sequence set

Synopsis

Prototype

const AjPStr ajSeqsetGetFormat (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

const AjPStr RETURN Sequence format

Input

seq:

(Input)

Sequence set object.

Returns

const AjPStr:

Sequence format

Description

Returns the sequence format for a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetOffend

Returns the sequence set offend value. This is the number of positions removed from the original end.

Synopsis

Prototype

ajint ajSeqsetGetOffend (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajint RETURN Sequence offend.

Input

seq:

(Input)

Sequence set object

Returns

ajint:

Sequence offend.

Description

Returns the sequence set offend value. This is the number of positions removed from the original end.

Availability

In release 6.4.0

Function ajSeqsetGetOffset

Returns the sequence set offset value. This is the number of positions removed from the original end.

Synopsis

Prototype

ajint ajSeqsetGetOffset (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajint RETURN Sequence offset.

Input

seq:

(Input)

Sequence set object

Returns

ajint:

Sequence offset.

Description

Returns the sequence set offset value. This is the number of positions removed from the original end.

Availability

In release 6.4.0

Function ajSeqsetGetRange

Returns the sequence range for a sequence set

Synopsis

Prototype

ajint ajSeqsetGetRange (
      const AjPSeqset seq,
      ajint* begin,
      ajint* end
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

ajint* begin Output Sequence range begin

ajint* end Output Sequence range end

ajint RETURN Sequence range length

Input

seq:

(Input)

Sequence set object.

Output

begin:	(Output)	Sequence range begin
end:	(Output)	Sequence range end

Returns

ajint:

Sequence range length

Description

Returns the sequence range for a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetTotlength

Returns the total number of bases or residues in a sequence set, ignoring any gap characters in aligned sequences.

Synopsis

Prototype

ajint ajSeqsetGetTotlength (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

ajint RETURN Total ungapped length

Input

seq:

(Input)

Sequence set object.

Returns

ajint:

Total ungapped length

Description

Returns the total number of bases or residues in a sequence set, ignoring any gap characters in aligned sequences.

Availability

In release 6.4.0

Function ajSeqsetGetUsa

Returns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const AjPStr ajSeqsetGetUsa (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence set object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Section: modifiers

These functions use the contents of a sequence set object and update them.

Functions: ajSeqsetFill ajSeqsetFmtLower ajSeqsetFmtUpper ajSeqsetReverse ajSeqsetSortLen ajSeqsetTrim

Function ajSeqsetFill

Fills a sequence set with gaps at the ends of any shorter sequences.

Synopsis

Prototype

ajint ajSeqsetFill (
      AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object to be set.

ajint RETURN Number of gaps inserted

Input & Output

seq:

(Modify)

Sequence set object to be set.

Returns

ajint:

Number of gaps inserted

Description

Fills a sequence set with gaps at the ends of any shorter sequences.

Availability

In release 6.4.0

Function ajSeqsetFmtLower

Converts all sequences in a set to lower case.

Synopsis

Prototype

void ajSeqsetFmtLower (
      AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object

void RETURN

Input & Output

seq:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Converts all sequences in a set to lower case.

Availability

In release 6.4.0

Function ajSeqsetFmtUpper

Converts all sequences in a set to upper case.

Synopsis

Prototype

void ajSeqsetFmtUpper (
      AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object

void RETURN

Input & Output

seq:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Converts all sequences in a set to upper case.

Availability

In release 6.4.0

Function ajSeqsetReverse

Reverse complements all sequences in a sequence set.

Synopsis

Prototype

void ajSeqsetReverse (
      AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object

void RETURN

Input & Output

seq:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Reverse complements all sequences in a sequence set.

Availability

In release 6.4.0

Function ajSeqsetSortLen

Sorts a sequence set by sequence length

Synopsis

Prototype

void ajSeqsetSortLen (
      AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object

void RETURN

Input & Output

seq:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Sorts a sequence set by sequence length

Availability

In release 6.4.0

Function ajSeqsetTrim

Trims a sequence set to start and end positions

Synopsis

Prototype

void ajSeqsetTrim (
      AjPSeqset seq
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object

void RETURN

Input & Output

seq:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Trims a sequence set to start and end positions

Availability

In release 6.4.0

Section: element assignment

Functions for assigning elements of a sequence set object.

Functions: ajSeqsetSetRange

Function ajSeqsetSetRange

Sets the start and end positions for a sequence set.

Synopsis

Prototype

void ajSeqsetSetRange (
      AjPSeqset seq,
      ajint pos1,
      ajint pos2
);

Type Name Read/Write Description

AjPSeqset seq Modify Sequence set object to be set.

ajint pos1 Input Start position. Negative values are from the end.

ajint pos2 Input End position. Negative values are from the end.

void RETURN

Input

pos1:	(Input)	Start position. Negative values are from the end.
pos2:	(Input)	End position. Negative values are from the end.

Input & Output

seq:

(Modify)

Sequence set object to be set.

Returns

void:

No return value

Description

Sets the start and end positions for a sequence set.

Availability

In release 6.4.0

Section: casts

These functions examine the contents of a sequence set object and return some derived information. Some of them provide access to the internal components of a sequence set object. They are provided for programming convenience but should be used with caution.

Functions: ajSeqsetGetBegin ajSeqsetGetEnd ajSeqsetGetLen ajSeqsetGetNameC ajSeqsetGetNameS ajSeqsetGetSeqarray ajSeqsetGetSize ajSeqsetGetTotweight ajSeqsetGetseqAccC ajSeqsetGetseqAccS ajSeqsetGetseqNameC ajSeqsetGetseqNameS ajSeqsetGetseqSeq ajSeqsetGetseqSeqC ajSeqsetGetseqSeqS ajSeqsetGetseqWeight

Function ajSeqsetGetBegin

Returns the sequence set start position, or 1 if no start has been set.

Synopsis

Prototype

ajuint ajSeqsetGetBegin (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint RETURN Start position.

Input

seq:

(Input)

Sequence set object

Returns

ajuint:

Start position.

Description

Returns the sequence set start position, or 1 if no start has been set.

Availability

In release 6.4.0

Function ajSeqsetGetEnd

Returns the sequence set end position, or the sequence length if no end has been set.

Synopsis

Prototype

ajuint ajSeqsetGetEnd (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint RETURN Start position.

Input

seq:

(Input)

Sequence set object

Returns

ajuint:

Start position.

Description

Returns the sequence set end position, or the sequence length if no end has been set.

Availability

In release 6.4.0

Function ajSeqsetGetLen

Returns the length of a sequence set, which is the maximum sequence length in the set.

Synopsis

Prototype

ajuint ajSeqsetGetLen (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint RETURN sequence set length.

Input

seq:

(Input)

Sequence set object

Returns

ajuint:

sequence set length.

Description

Returns the length of a sequence set, which is the maximum sequence length in the set.

Availability

In release 6.4.0

Function ajSeqsetGetNameC

Synopsis

Prototype

const char* ajSeqsetGetNameC (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

const char* RETURN Name as a C character string.

Input

seq:

(Input)

Sequence set object.

Returns

const char*:

Name as a C character string.

Description

Availability

In release 6.4.0

Function ajSeqsetGetNameS

Synopsis

Prototype

const AjPStr ajSeqsetGetNameS (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

const AjPStr RETURN Name as a string.

Input

seq:

(Input)

Sequence set object.

Returns

const AjPStr:

Name as a string.

Description

Availability

In release 6.4.0

Function ajSeqsetGetSeqarray

Returns an array of sequences. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.

The array is 1 larger than the sequence set, with the last element set to NULL.

Synopsis

Prototype

AjPSeq* ajSeqsetGetSeqarray (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

AjPSeq* RETURN Sequence object.

Input

seq:

(Input)

Sequence set object.

Returns

AjPSeq*:

Sequence object.

Description

The array is 1 larger than the sequence set, with the last element set to NULL.

Availability

In release 6.4.0

Function ajSeqsetGetSize

Returns the number of sequences in a sequence set

Synopsis

Prototype

ajuint ajSeqsetGetSize (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint RETURN sequence set size.

Input

seq:

(Input)

Sequence set object

Returns

ajuint:

sequence set size.

Description

Returns the number of sequences in a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetTotweight

Returns the weight of all sequences in a sequence set

Synopsis

Prototype

float ajSeqsetGetTotweight (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

float RETURN sequence weight as a float.

Input

seq:

(Input)

Sequence set object

Returns

float:

sequence weight as a float.

Description

Returns the weight of all sequences in a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetseqAccC

Returns the accession number of a sequence in a sequence set

Synopsis

Prototype

const char* ajSeqsetGetseqAccC (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint i Input Sequence index

const char* RETURN accession number as a string.

Input

seq:	(Input)	Sequence set object
i:	(Input)	Sequence index

Returns

const char*:

accession number as a string.

Description

Returns the accession number of a sequence in a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetseqAccS

Returns the accession number of a sequence in a sequence set

Synopsis

Prototype

const AjPStr ajSeqsetGetseqAccS (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint i Input Sequence index

const AjPStr RETURN accession number as a string.

Input

seq:	(Input)	Sequence set object
i:	(Input)	Sequence index

Returns

const AjPStr:

accession number as a string.

Description

Returns the accession number of a sequence in a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetseqNameC

Returns the name of a sequence in a sequence set

Synopsis

Prototype

const char* ajSeqsetGetseqNameC (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint i Input Sequence index

const char* RETURN sequence name as a string.

Input

seq:	(Input)	Sequence set object
i:	(Input)	Sequence index

Returns

const char*:

sequence name as a string.

Description

Returns the name of a sequence in a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetseqNameS

Returns the name of a sequence in a sequence set

Synopsis

Prototype

const AjPStr ajSeqsetGetseqNameS (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint i Input Sequence index

const AjPStr RETURN sequence name as a string.

Input

seq:	(Input)	Sequence set object
i:	(Input)	Sequence index

Returns

const AjPStr:

sequence name as a string.

Description

Returns the name of a sequence in a sequence set

Availability

In release 6.4.0

Function ajSeqsetGetseqSeq

Returns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.

Synopsis

Prototype

const AjPSeq ajSeqsetGetseqSeq (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

ajuint i Input Sequence index number in set

const AjPSeq RETURN Sequence object.

Input

seq:	(Input)	Sequence set object.
i:	(Input)	Sequence index number in set

Returns

const AjPSeq:

Sequence object.

Description

Availability

In release 6.4.0

Function ajSeqsetGetseqSeqC

Synopsis

Prototype

const char* ajSeqsetGetseqSeqC (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

ajuint i Input Sequence index number in set

const char* RETURN Sequence as a C string.

Input

seq:	(Input)	Sequence set object.
i:	(Input)	Sequence index number in set

Returns

const char*:

Sequence as a C string.

Description

Availability

In release 6.4.0

Function ajSeqsetGetseqSeqS

Synopsis

Prototype

const AjPStr ajSeqsetGetseqSeqS (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object.

ajuint i Input Sequence index number in set

const AjPStr RETURN Sequence object.

Input

seq:	(Input)	Sequence set object.
i:	(Input)	Sequence index number in set

Returns

const AjPStr:

Sequence object.

Description

Availability

In release 6.4.0

Function ajSeqsetGetseqWeight

Returns the weight of a sequence in a sequence set

Synopsis

Prototype

float ajSeqsetGetseqWeight (
      const AjPSeqset seq,
      ajuint i
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set object

ajuint i Input Sequence index

float RETURN sequence weight as a float.

Input

seq:	(Input)	Sequence set object
i:	(Input)	Sequence index

Returns

float:

sequence weight as a float.

Description

Returns the weight of a sequence in a sequence set

Availability

In release 6.4.0

Section: testing properties

Tests properties of a sequence set

Functions: ajSeqsetIsDna ajSeqsetIsNuc ajSeqsetIsProt ajSeqsetIsRna

Function ajSeqsetIsDna

Tests whether a sequence set is DNA.

Synopsis

Prototype

AjBool ajSeqsetIsDna (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set

AjBool RETURN ajTrue for a nucleotide sequence set.

Input

seq:

(Input)

Sequence set

Returns

AjBool:

ajTrue for a nucleotide sequence set.

Description

Tests whether a sequence set is DNA.

Availability

In release 6.4.0

Function ajSeqsetIsNuc

Tests whether a sequence set is nucleotide.

Synopsis

Prototype

AjBool ajSeqsetIsNuc (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set

AjBool RETURN ajTrue for a nucleotide sequence set.

Input

seq:

(Input)

Sequence set

Returns

AjBool:

ajTrue for a nucleotide sequence set.

Description

Tests whether a sequence set is nucleotide.

Availability

In release 6.4.0

Function ajSeqsetIsProt

Tests whether a sequence set is protein.

Synopsis

Prototype

AjBool ajSeqsetIsProt (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set

AjBool RETURN ajTrue for a protein sequence set.

Input

seq:

(Input)

Sequence set

Returns

AjBool:

ajTrue for a protein sequence set.

Description

Tests whether a sequence set is protein.

Availability

In release 6.4.0

Function ajSeqsetIsRna

Tests whether a sequence set is RNA.

Synopsis

Prototype

AjBool ajSeqsetIsRna (
      const AjPSeqset seq
);

Type Name Read/Write Description

const AjPSeqset seq Input Sequence set

AjBool RETURN ajTrue for a nucleotide sequence set.

Input

seq:

(Input)

Sequence set

Returns

AjBool:

ajTrue for a nucleotide sequence set.

Description

Tests whether a sequence set is RNA.

Availability

In release 6.4.0

Datatype: AjPStr

sequence strings

Sections: conversion

Section: conversion

Convert sequence to numbers for efficient processing

Functions: ajSeqstrConvertNum

Function ajSeqstrConvertNum

Converts a string of sequence characters to numbers using a conversion table.

Synopsis

Prototype

AjBool ajSeqstrConvertNum (
      const AjPStr seq,
      const AjPSeqCvt cvt,
      AjPStr* Pnumseq
);

Type Name Read/Write Description

const AjPStr seq Input Sequence as a string

const AjPSeqCvt cvt Input Conversion table.

AjPStr* Pnumseq Output Output numeric version of the sequence.

AjBool RETURN ajTrue on success.

Input

seq:	(Input)	Sequence as a string
cvt:	(Input)	Conversion table.

Output

Pnumseq:

(Output)

Output numeric version of the sequence.

Returns

AjBool:

ajTrue on success.

Description

Converts a string of sequence characters to numbers using a conversion table.

Availability

In release 6.4.0

Datatype: AjPSeqCvt

sequence conversion

Sections: Sequence Conversion Functions constructors Sequence Destructors element retrieval

Section: Sequence Conversion Functions

Functions: ajSeqcvtTrace

Function ajSeqcvtTrace

Traces a conversion table with debug calls.

Synopsis

Prototype

void ajSeqcvtTrace (
      const AjPSeqCvt cvt
);

Type Name Read/Write Description

const AjPSeqCvt cvt Input Conversion table.

void RETURN

Input

cvt:

(Input)

Conversion table.

Returns

void:

No return value

Description

Traces a conversion table with debug calls.

Availability

In release 6.4.0

Section: constructors

Functions: ajSeqcvtNewC ajSeqcvtNewEndC ajSeqcvtNewNumberC ajSeqcvtNewStr ajSeqcvtNewStrAsym

Function ajSeqcvtNewC

Generates a new conversion table in which the first character in the string provided is converted to 1, the second to 2, and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero.

Synopsis

Prototype

AjPSeqCvt ajSeqcvtNewC (
      const char* bases
);

Type Name Read/Write Description

const char* bases Input Allowed sequence characters.

AjPSeqCvt RETURN Conversion table.

Input

bases:

(Input)

Allowed sequence characters.

Returns

AjPSeqCvt:

Conversion table.

Description

Availability

In release 6.4.0

Function ajSeqcvtNewEndC

Generates a new conversion table in which the first character in the string provided is converted to 0, the second to 1, and so on. Upper and lower case characters are converted to the same numbers. All other characters are converted to one more than the highest char.

Synopsis

Prototype

AjPSeqCvt ajSeqcvtNewEndC (
      const char* bases
);

Type Name Read/Write Description

const char* bases Input Allowed sequence characters.

AjPSeqCvt RETURN Conversion table.

Input

bases:

(Input)

Allowed sequence characters.

Returns

AjPSeqCvt:

Conversion table.

Description

Availability

In release 6.4.0

Function ajSeqcvtNewNumberC

Generates a new conversion table in which the characters are retained as upper case, numbers are set to -1 and all other characters are set to -2.

Synopsis

Prototype

AjPSeqCvt ajSeqcvtNewNumberC (
      const char* bases
);

Type Name Read/Write Description

const char* bases Input Allowed sequence characters.

AjPSeqCvt RETURN Conversion table.

Input

bases:

(Input)

Allowed sequence characters.

Returns

AjPSeqCvt:

Conversion table.

Description

Generates a new conversion table in which the characters are retained as upper case, numbers are set to -1 and all other characters are set to -2.

Availability

In release 6.4.0

Function ajSeqcvtNewStr

Generates a new conversion table in which the first character of the first string in the array provided is converted to 1, the first character of the second string is converted to 2, the first character of the third string is converted to 3 and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero.

Synopsis

Prototype

AjPSeqCvt ajSeqcvtNewStr (
      const AjPPStr basearray,
      ajint numbases
);

Type Name Read/Write Description

const AjPPStr basearray Input Allowed sequence character strings (size specified by parameter n)

ajint numbases Input Number of strings

AjPSeqCvt RETURN Conversion table.

Input

basearray:	(Input)	Allowed sequence character strings (size specified by parameter n)
numbases:	(Input)	Number of strings

Returns

AjPSeqCvt:

Conversion table.

Description

Availability

In release 6.4.0

Function ajSeqcvtNewStrAsym

Synopsis

Prototype

AjPSeqCvt ajSeqcvtNewStrAsym (
      const AjPPStr basearray,
      ajint numbases,
      const AjPPStr matchbases,
      ajint nummatch
);

Type Name Read/Write Description

const AjPPStr basearray Input Allowed sequence character strings (size specified by parameter n)

ajint numbases Input Number of strings

const AjPPStr matchbases Input Allowed sequence character strings for rows (size specified by parameter rn)

ajint nummatch Input Number of strings (rows)

AjPSeqCvt RETURN Conversion table.

Input

basearray:	(Input)	Allowed sequence character strings (size specified by parameter n)
numbases:	(Input)	Number of strings
matchbases:	(Input)	Allowed sequence character strings for rows (size specified by parameter rn)
nummatch:	(Input)	Number of strings (rows)

Returns

AjPSeqCvt:

Conversion table.

Description

Availability

In release 6.4.0

Section: Sequence Destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions: ajSeqcvtDel

Function ajSeqcvtDel

Delete a conversion table

Synopsis

Prototype

void ajSeqcvtDel (
      AjPSeqCvt* Pcvt
);

Type Name Read/Write Description

AjPSeqCvt* Pcvt Output Conversion table reference

void RETURN

Output

Pcvt:

(Output)

Conversion table reference

Returns

void:

No return value

Description

Delete a conversion table

Availability

In release 6.4.0

Section: element retrieval

These functions use the contents of a sequence conversion object

Functions: ajSeqcvtGetCodeK ajSeqcvtGetCodeS ajSeqcvtGetCodeAsymS ajSeqcvtGetCodeAsymrowS ajSeqcvtGetLen

Function ajSeqcvtGetCodeK

Returns the integer code corresponding to a sequence character in a conversion table

Synopsis

Prototype

ajint ajSeqcvtGetCodeK (
      const AjPSeqCvt cvt,
      char ch
);

Type Name Read/Write Description

const AjPSeqCvt cvt Input Conversion table

char ch Input Sequence character

ajint RETURN Conversion code

Input

cvt:	(Input)	Conversion table
ch:	(Input)	Sequence character

Returns

ajint:

Conversion code

Description

Returns the integer code corresponding to a sequence character in a conversion table

Availability

In release 6.4.0

Function ajSeqcvtGetCodeS

Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).

Synopsis

Prototype

ajint ajSeqcvtGetCodeS (
      const AjPSeqCvt cvt,
      const AjPStr str
);

Type Name Read/Write Description

const AjPSeqCvt cvt Input Conversion table

const AjPStr str Input Sequence character string

ajint RETURN Conversion code

Input

cvt:	(Input)	Conversion table
str:	(Input)	Sequence character string

Returns

ajint:

Conversion code

Description

Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).

Availability

In release 6.4.0

Function ajSeqcvtGetCodeAsymS

Returns the integer code corresponding to a sequence character string in a conversion table (for columns in asymmetrical matrices).

Synopsis

Prototype

ajint ajSeqcvtGetCodeAsymS (
      const AjPSeqCvt cvt,
      const AjPStr str
);

Type Name Read/Write Description

const AjPSeqCvt cvt Input Conversion table

const AjPStr str Input Sequence character string

ajint RETURN Conversion code

Input

cvt:	(Input)	Conversion table
str:	(Input)	Sequence character string

Returns

ajint:

Conversion code

Description

Returns the integer code corresponding to a sequence character string in a conversion table (for columns in asymmetrical matrices).

Availability

In release 6.4.0

Function ajSeqcvtGetCodeAsymrowS

Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).

Synopsis

Prototype

ajint ajSeqcvtGetCodeAsymrowS (
      const AjPSeqCvt cvt,
      const AjPStr str
);

Type Name Read/Write Description

const AjPSeqCvt cvt Input Conversion table

const AjPStr str Input Sequence character string

ajint RETURN Conversion code

Input

cvt:	(Input)	Conversion table
str:	(Input)	Sequence character string

Returns

ajint:

Conversion code

Description

Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).

Availability

In release 6.4.0

Function ajSeqcvtGetLen

Returns the length of a conversion table string (number of sequence characters explicitly included)

Synopsis

Prototype

ajuint ajSeqcvtGetLen (
      const AjPSeqCvt cvt
);

Type Name Read/Write Description

const AjPSeqCvt cvt Input Conversion table

ajuint RETURN Length

Input

cvt:

(Input)

Conversion table

Returns

ajuint:

Length

Description

Returns the length of a conversion table string (number of sequence characters explicitly included)

Availability

In release 6.4.0

Datatype: AjPSeqDate

sequence dates

Sections: sequence date constructors destructors modifiers

Section: sequence date constructors

Functions: ajSeqdateNew ajSeqdateNewDate

Function ajSeqdateNew

Constructor for empty sequence date object

Synopsis

Prototype

AjPSeqDate ajSeqdateNew (
      void
);

Type Name Read/Write Description

AjPSeqDate RETURN Empty sequence date object

Returns

AjPSeqDate:

Empty sequence date object

Description

Constructor for empty sequence date object

Availability

In release 6.4.0

Function ajSeqdateNewDate

Constructor for copy of a sequence date object

Synopsis

Prototype

AjPSeqDate ajSeqdateNewDate (
      const AjPSeqDate date
);

Type Name Read/Write Description

const AjPSeqDate date Input Sequence date object

AjPSeqDate RETURN Empty sequence date object

Input

date:

(Input)

Sequence date object

Returns

AjPSeqDate:

Empty sequence date object

Description

Constructor for copy of a sequence date object

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions: ajSeqdateDel

Function ajSeqdateDel

Deletes a sequence date object.

Synopsis

Prototype

void ajSeqdateDel (
      AjPSeqDate* Pdate
);

Type Name Read/Write Description

AjPSeqDate* Pdate Delete Sequence date object

void RETURN

Output

Pdate:

(Delete)

Sequence date object

Returns

void:

No return value

Description

Deletes a sequence date object.

Availability

In release 6.4.0

Section: modifiers

These functions update contents of a sequence date object.

Functions: ajSeqdateClear ajSeqdateSetCreateS ajSeqdateSetModifyS ajSeqdateSetModseqS

Function ajSeqdateClear

Resets all data for a sequence date object.

Synopsis

Prototype

void ajSeqdateClear (
      AjPSeqDate date
);

Type Name Read/Write Description

AjPSeqDate date Modify Sequence date object

void RETURN

Input & Output

date:

(Modify)

Sequence date object

Returns

void:

No return value

Description

Resets all data for a sequence date object.

Availability

In release 6.4.0

Function ajSeqdateSetCreateS

Set the sequence creation date

Synopsis

Prototype

AjBool ajSeqdateSetCreateS (
      AjPSeqDate date,
      const AjPStr datestr
);

Type Name Read/Write Description

AjPSeqDate date Output Sequence date

const AjPStr datestr Input Date string

AjBool RETURN ajTrue on success

Input

datestr:

(Input)

Date string

Output

date:

(Output)

Sequence date

Returns

AjBool:

ajTrue on success

Description

Set the sequence creation date

Availability

In release 6.4.0

Function ajSeqdateSetModifyS

Set the entry modification date

Synopsis

Prototype

AjBool ajSeqdateSetModifyS (
      AjPSeqDate date,
      const AjPStr datestr
);

Type Name Read/Write Description

AjPSeqDate date Output Sequence date

const AjPStr datestr Input Date string

AjBool RETURN ajTrue on success

Input

datestr:

(Input)

Date string

Output

date:

(Output)

Sequence date

Returns

AjBool:

ajTrue on success

Description

Set the entry modification date

Availability

In release 6.4.0

Function ajSeqdateSetModseqS

Set the sequence modification date

Synopsis

Prototype

AjBool ajSeqdateSetModseqS (
      AjPSeqDate date,
      const AjPStr datestr
);

Type Name Read/Write Description

AjPSeqDate date Output Sequence date

const AjPStr datestr Input Date string

AjBool RETURN ajTrue on success

Input

datestr:

(Input)

Date string

Output

date:

(Output)

Sequence date

Returns

AjBool:

ajTrue on success

Description

Set the sequence modification date

Availability

In release 6.4.0

Datatype: AjPSeqDesc

sequence descriptions

Sections: descriptions constructors destructors modifiers

Section: descriptions constructors

Functions: ajSeqdescNew ajSeqdescNewDesc

Function ajSeqdescNew

Constructor for empty description object

Synopsis

Prototype

AjPSeqDesc ajSeqdescNew (
      void
);

Type Name Read/Write Description

AjPSeqDesc RETURN Empty sequence description object

Returns

AjPSeqDesc:

Empty sequence description object

Description

Constructor for empty description object

Availability

In release 6.4.0

Function ajSeqdescNewDesc

Constructor for copy of a description object

Synopsis

Prototype

AjPSeqDesc ajSeqdescNewDesc (
      const AjPSeqDesc desc
);

Type Name Read/Write Description

const AjPSeqDesc desc Input Description object

AjPSeqDesc RETURN Copied description object

Input

desc:

(Input)

Description object

Returns

AjPSeqDesc:

Copied description object

Description

Constructor for copy of a description object

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for a description object

Functions: ajSeqdescDel

Function ajSeqdescDel

Deletes a description object.

Synopsis

Prototype

void ajSeqdescDel (
      AjPSeqDesc* Pdesc
);

Type Name Read/Write Description

AjPSeqDesc* Pdesc Delete Description object

void RETURN

Output

Pdesc:

(Delete)

Description object

Returns

void:

No return value

Description

Deletes a description object.

Availability

In release 6.4.0

Section: modifiers

These functions update contents of a description object.

Functions: ajSeqdescAppendName ajSeqdescClear ajSeqdescSetName

Function ajSeqdescAppendName

Append to the name of a description

Synopsis

Prototype

AjBool ajSeqdescAppendName (
      AjPSeqDesc desc,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqDesc desc Modify Description object

const AjPStr str Input Name string

AjBool RETURN True on success

Input

str:

(Input)

Name string

Input & Output

desc:

(Modify)

Description object

Returns

AjBool:

True on success

Description

Append to the name of a description

Availability

In release 6.4.0

Function ajSeqdescClear

Resets data for a description object.

Synopsis

Prototype

void ajSeqdescClear (
      AjPSeqDesc desc
);

Type Name Read/Write Description

AjPSeqDesc desc Modify Description object

void RETURN

Input & Output

desc:

(Modify)

Description object

Returns

void:

No return value

Description

Resets data for a description object.

Availability

In release 6.4.0

Function ajSeqdescSetName

Set the name of a description object

Synopsis

Prototype

AjBool ajSeqdescSetName (
      AjPSeqDesc desc,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqDesc desc Modify Description object

const AjPStr str Input Synonyms string

AjBool RETURN True on success

Input

str:

(Input)

Synonyms string

Input & Output

desc:

(Modify)

Description object

Returns

AjBool:

True on success

Description

Set the name of a description object

Availability

In release 6.4.0

Datatype: AjPList

Description list operations

Sections: Description list operations

Section: Description list operations

Manipulating lists of descriptions

Functions: ajSeqdesclistClone

Function ajSeqdesclistClone

Copy a list of genes to another list

Synopsis

Prototype

AjBool ajSeqdesclistClone (
      const AjPList src,
      AjPList dest
);

Type Name Read/Write Description

const AjPList src Input Source list of descriptions

AjPList dest Output Destination list of descriptions

AjBool RETURN True on success

Input

src:

(Input)

Source list of descriptions

Output

dest:

(Output)

Destination list of descriptions

Returns

AjBool:

True on success

Description

Copy a list of genes to another list

Availability

In release 6.4.0

Datatype: AjPSeqSubdesc

sequence sub-descriptions

Sections: sub-descriptions constructors destructors modifiers

Section: sub-descriptions constructors

Functions: ajSeqsubdescNew ajSeqsubdescNewSubdesc

Function ajSeqsubdescNew

Constructor for empty sub-description object

Synopsis

Prototype

AjPSeqSubdesc ajSeqsubdescNew (
      void
);

Type Name Read/Write Description

AjPSeqSubdesc RETURN Empty sequence sub-description object

Returns

AjPSeqSubdesc:

Empty sequence sub-description object

Description

Constructor for empty sub-description object

Availability

In release 6.4.0

Function ajSeqsubdescNewSubdesc

Constructor for copy of a sub-description object

Synopsis

Prototype

AjPSeqSubdesc ajSeqsubdescNewSubdesc (
      const AjPSeqSubdesc desc
);

Type Name Read/Write Description

const AjPSeqSubdesc desc Input Sub-description object

AjPSeqSubdesc RETURN Copied sub-description object

Input

desc:

(Input)

Sub-description object

Returns

AjPSeqSubdesc:

Copied sub-description object

Description

Constructor for copy of a sub-description object

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for a sub-description object

Functions: ajSeqsubdescDel

Function ajSeqsubdescDel

Deletes a sub-description object.

Synopsis

Prototype

void ajSeqsubdescDel (
      AjPSeqSubdesc* Pdesc
);

Type Name Read/Write Description

AjPSeqSubdesc* Pdesc Delete Sub-description object

void RETURN

Output

Pdesc:

(Delete)

Sub-description object

Returns

void:

No return value

Description

Deletes a sub-description object.

Availability

In release 6.4.0

Section: modifiers

These functions update contents of a sub-description object.

Functions: ajSeqsubdescAppendName ajSeqsubdescClear ajSeqsubdescSetName

Function ajSeqsubdescAppendName

Append to the name of a description

Synopsis

Prototype

AjBool ajSeqsubdescAppendName (
      AjPSeqSubdesc desc,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqSubdesc desc Modify Description object

const AjPStr str Input Name string

AjBool RETURN True on success

Input

str:

(Input)

Name string

Input & Output

desc:

(Modify)

Description object

Returns

AjBool:

True on success

Description

Append to the name of a description

Availability

In release 6.4.0

Function ajSeqsubdescClear

Resets data for a sub-description object.

Synopsis

Prototype

void ajSeqsubdescClear (
      AjPSeqSubdesc desc
);

Type Name Read/Write Description

AjPSeqSubdesc desc Modify Sub-description object

void RETURN

Input & Output

desc:

(Modify)

Sub-description object

Returns

void:

No return value

Description

Resets data for a sub-description object.

Availability

In release 6.4.0

Function ajSeqsubdescSetName

Set the name of a sub-description object

Synopsis

Prototype

AjBool ajSeqsubdescSetName (
      AjPSeqSubdesc desc,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqSubdesc desc Modify Sub-description object

const AjPStr str Input Synonyms string

AjBool RETURN True on success

Input

str:

(Input)

Synonyms string

Input & Output

desc:

(Modify)

Sub-description object

Returns

AjBool:

True on success

Description

Set the name of a sub-description object

Availability

In release 6.4.0

Datatype: AjPList

Description list operations

Sections: Description list operations

Section: Description list operations

Manipulating lists of sub-descriptions

Functions: ajSeqsubdesclistClone

Function ajSeqsubdesclistClone

Copy a list of sub-descriptions to another list

Synopsis

Prototype

AjBool ajSeqsubdesclistClone (
      const AjPList src,
      AjPList dest
);

Type Name Read/Write Description

const AjPList src Input Source list of sub-descriptions

AjPList dest Output Destination list of sub-descriptions

AjBool RETURN True on success

Input

src:

(Input)

Source list of sub-descriptions

Output

dest:

(Output)

Destination list of sub-descriptions

Returns

AjBool:

True on success

Description

Copy a list of sub-descriptions to another list

Availability

In release 6.4.0

Datatype: AjPSeqGene

gene names

Sections: gene names constructors destructors modifiers

Section: gene names constructors

Functions: ajSeqgeneNew ajSeqgeneNewGene ajSeqgeneNewName

Function ajSeqgeneNew

Constructor for empty gene object

Synopsis

Prototype

AjPSeqGene ajSeqgeneNew (
      void
);

Type Name Read/Write Description

AjPSeqGene RETURN Empty sequence gene object

Returns

AjPSeqGene:

Empty sequence gene object

Description

Constructor for empty gene object

Availability

In release 6.4.0

Function ajSeqgeneNewGene

Constructor for copy of a gene object

Synopsis

Prototype

AjPSeqGene ajSeqgeneNewGene (
      const AjPSeqGene gene
);

Type Name Read/Write Description

const AjPSeqGene gene Input Gene object

AjPSeqGene RETURN Copied gene object

Input

gene:

(Input)

Gene object

Returns

AjPSeqGene:

Copied gene object

Description

Constructor for copy of a gene object

Availability

In release 6.4.0

Function ajSeqgeneNewName

Constructor for gene with given name

Synopsis

Prototype

AjPSeqGene ajSeqgeneNewName (
      const AjPStr str
);

Type Name Read/Write Description

const AjPStr str Input Gene name

AjPSeqGene RETURN New gene object

Input

str:

(Input)

Gene name

Returns

AjPSeqGene:

New gene object

Description

Constructor for gene with given name

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for a gene object

Functions: ajSeqgeneDel

Function ajSeqgeneDel

Deletes a gene object.

Synopsis

Prototype

void ajSeqgeneDel (
      AjPSeqGene* Pgene
);

Type Name Read/Write Description

AjPSeqGene* Pgene Delete Gene object

void RETURN

Output

Pgene:

(Delete)

Gene object

Returns

void:

No return value

Description

Deletes a gene object.

Availability

In release 6.4.0

Section: modifiers

These functions update contents of a gene object.

Functions: ajSeqgeneAppendName ajSeqgeneAppendOln ajSeqgeneAppendOrf ajSeqgeneAppendSynonyms ajSeqgeneSetName ajSeqgeneSetOln ajSeqgeneSetOrf ajSeqgeneSetSynonyms

Function ajSeqgeneAppendName

Append to the name of a gene

Synopsis

Prototype

AjBool ajSeqgeneAppendName (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input Name string

AjBool RETURN True on success

Input

str:

(Input)

Name string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Append to the name of a gene

Availability

In release 6.4.0

Function ajSeqgeneAppendOln

Append to ordered locus names of a gene

Synopsis

Prototype

AjBool ajSeqgeneAppendOln (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input Ordered locus names string

AjBool RETURN True on success

Input

str:

(Input)

Ordered locus names string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Append to ordered locus names of a gene

Availability

In release 6.4.0

Function ajSeqgeneAppendOrf

Append to the ORF name of a gene

Synopsis

Prototype

AjBool ajSeqgeneAppendOrf (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input ORF name string

AjBool RETURN True on success

Input

str:

(Input)

ORF name string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Append to the ORF name of a gene

Availability

In release 6.4.0

Function ajSeqgeneAppendSynonyms

Append to the name of a gene

Synopsis

Prototype

AjBool ajSeqgeneAppendSynonyms (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input Synonyms string

AjBool RETURN True on success

Input

str:

(Input)

Synonyms string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Append to the name of a gene

Availability

In release 6.4.0

Function ajSeqgeneSetName

Set the name of a gene

Synopsis

Prototype

AjBool ajSeqgeneSetName (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input Name string

AjBool RETURN True on success

Input

str:

(Input)

Name string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Set the name of a gene

Availability

In release 6.4.0

Function ajSeqgeneSetOln

Set the ordered locus names of a gene

Synopsis

Prototype

AjBool ajSeqgeneSetOln (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input Ordered locus names string

AjBool RETURN True on success

Input

str:

(Input)

Ordered locus names string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Set the ordered locus names of a gene

Availability

In release 6.4.0

Function ajSeqgeneSetOrf

Set the ORF name of a gene

Synopsis

Prototype

AjBool ajSeqgeneSetOrf (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input ORF name string

AjBool RETURN True on success

Input

str:

(Input)

ORF name string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Set the ORF name of a gene

Availability

In release 6.4.0

Function ajSeqgeneSetSynonyms

Set the name of a gene

Synopsis

Prototype

AjBool ajSeqgeneSetSynonyms (
      AjPSeqGene gene,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqGene gene Modify Gene object

const AjPStr str Input Synonyms string

AjBool RETURN True on success

Input

str:

(Input)

Synonyms string

Input & Output

gene:

(Modify)

Gene object

Returns

AjBool:

True on success

Description

Set the name of a gene

Availability

In release 6.4.0

Datatype: AjPList

Reference list operations

Sections: Reference list operations

Section: Reference list operations

Manipulating lists of genes

Functions: ajSeqgenelistClone

Function ajSeqgenelistClone

Copy a list of genes to another list

Synopsis

Prototype

AjBool ajSeqgenelistClone (
      const AjPList src,
      AjPList dest
);

Type Name Read/Write Description

const AjPList src Input Source list of genes

AjPList dest Output Destination list of genes

AjBool RETURN True on success

Input

src:

(Input)

Source list of genes

Output

dest:

(Output)

Destination list of genes

Returns

AjBool:

True on success

Description

Copy a list of genes to another list

Availability

In release 6.4.0

Datatype: AjPSeqXref

sequence citations

Sections: sequence cross-reference constructors destructors

Section: sequence cross-reference constructors

Functions: ajSeqxrefNew ajSeqxrefNewDbC ajSeqxrefNewDbS ajSeqxrefNewRef

Function ajSeqxrefNew

Constructor for empty sequence citation object

Synopsis

Prototype

AjPSeqXref ajSeqxrefNew (
      void
);

Type Name Read/Write Description

AjPSeqXref RETURN Empty sequence cross-reference object

Returns

AjPSeqXref:

Empty sequence cross-reference object

Description

Constructor for empty sequence citation object

Availability

In release 6.4.0

Function ajSeqxrefNewDbC

Constructor for copy of a sequence citation object

Synopsis

Prototype

AjPSeqXref ajSeqxrefNewDbC (
      const AjPStr id,
      const char* db,
      ajuint reftype
);

Type Name Read/Write Description

const AjPStr id Input Primary identifier

const char* db Input Database name

ajuint reftype Input Reference type

AjPSeqXref RETURN New sequence cross-reference object

Input

id:	(Input)	Primary identifier
db:	(Input)	Database name
reftype:	(Input)	Reference type

Returns

AjPSeqXref:

New sequence cross-reference object

Description

Constructor for copy of a sequence citation object

Availability

In release 6.4.0

Function ajSeqxrefNewDbS

Constructor for copy of a sequence citation object

Synopsis

Prototype

AjPSeqXref ajSeqxrefNewDbS (
      const AjPStr id,
      const AjPStr db,
      ajuint reftype
);

Type Name Read/Write Description

const AjPStr id Input Primary identifier

const AjPStr db Input Database name

ajuint reftype Input Reference type

AjPSeqXref RETURN New sequence cross-reference object

Input

id:	(Input)	Primary identifier
db:	(Input)	Database name
reftype:	(Input)	Reference type

Returns

AjPSeqXref:

New sequence cross-reference object

Description

Constructor for copy of a sequence citation object

Availability

In release 6.4.0

Function ajSeqxrefNewRef

Constructor for copy of a sequence citation object

Synopsis

Prototype

AjPSeqXref ajSeqxrefNewRef (
      const AjPSeqXref xref
);

Type Name Read/Write Description

const AjPSeqXref xref Input Sequence cross-reference object

AjPSeqXref RETURN Copied sequence cross-reference object

Input

xref:

(Input)

Sequence cross-reference object

Returns

AjPSeqXref:

Copied sequence cross-reference object

Description

Constructor for copy of a sequence citation object

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence cross-reference

Functions: ajSeqxrefDel

Function ajSeqxrefDel

Deletes a sequence cross-reference object.

Synopsis

Prototype

void ajSeqxrefDel (
      AjPSeqXref* Pxref
);

Type Name Read/Write Description

AjPSeqXref* Pxref Delete Sequence cross-reference object

void RETURN

Output

Pxref:

(Delete)

Sequence cross-reference object

Returns

void:

No return value

Description

Deletes a sequence cross-reference object.

Availability

In release 6.4.0

Datatype: AjPList

Cross-reference list operations

Sections: Reference list operations

Section: Reference list operations

Manipulating lists of sequence cross-references

Functions: ajSeqxreflistClone

Function ajSeqxreflistClone

Copy a list of cross-references to another list

Synopsis

Prototype

AjBool ajSeqxreflistClone (
      const AjPList src,
      AjPList dest
);

Type Name Read/Write Description

const AjPList src Input Source list of cross-references

AjPList dest Output Destination list of cross-references

AjBool RETURN True on success

Input

src:

(Input)

Source list of cross-references

Output

dest:

(Output)

Destination list of cross-references

Returns

AjBool:

True on success

Description

Copy a list of cross-references to another list

Availability

In release 6.4.0

Function ajSeqxreflistSort

Sort a list of cross-references

Synopsis

Prototype

AjBool ajSeqxreflistSort (
      AjPList list
);

Type Name Read/Write Description

AjPList list Modify Source list of cross-references

AjBool RETURN True on success

Input & Output

list:

(Modify)

Source list of cross-references

Returns

AjBool:

True on success

Description

Sort a list of cross-references

Availability

In release 6.4.0

Datatype: AjPSeqRef

sequence citations

Sections: sequence citation constructors destructors modifiers

Section: sequence citation constructors

Functions: ajSeqrefNew ajSeqrefNewRef

Function ajSeqrefNew

Constructor for empty sequence citation object

Synopsis

Prototype

AjPSeqRef ajSeqrefNew (
      void
);

Type Name Read/Write Description

AjPSeqRef RETURN Empty sequence citation object

Returns

AjPSeqRef:

Empty sequence citation object

Description

Constructor for empty sequence citation object

Availability

In release 6.4.0

Function ajSeqrefNewRef

Constructor for copy of a sequence citation object

Synopsis

Prototype

AjPSeqRef ajSeqrefNewRef (
      const AjPSeqRef ref
);

Type Name Read/Write Description

const AjPSeqRef ref Input Sequence citation object

AjPSeqRef RETURN Copied sequence citation object

Input

ref:

(Input)

Sequence citation object

Returns

AjPSeqRef:

Copied sequence citation object

Description

Constructor for copy of a sequence citation object

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence citation

Functions: ajSeqrefDel

Function ajSeqrefDel

Deletes a sequence citation object.

Synopsis

Prototype

void ajSeqrefDel (
      AjPSeqRef* Pref
);

Type Name Read/Write Description

AjPSeqRef* Pref Delete Sequence citation object

void RETURN

Output

Pref:

(Delete)

Sequence citation object

Returns

void:

No return value

Description

Deletes a sequence citation object.

Availability

In release 6.4.0

Section: modifiers

These functions update contents of a sequence citation object.

Functions: ajSeqrefAppendAuthors ajSeqrefAppendComment ajSeqrefAppendGroupname ajSeqrefAppendLocation ajSeqrefAppendPosition ajSeqrefAppendTitle ajSeqrefAppendXref ajSeqrefFmtAuthorsEmbl ajSeqrefFmtAuthorsGb ajSeqrefFmtLocationEmbl ajSeqrefFmtLocationGb ajSeqrefFmtTitleGb ajSeqrefSetAuthors ajSeqrefSetComment ajSeqrefSetGroupname ajSeqrefSetLocation ajSeqrefSetLoctype ajSeqrefSetPosition ajSeqrefSetTitle ajSeqrefSetXref ajSeqrefSetnumNumber ajSeqrefStandard

Function ajSeqrefAppendAuthors

Append to the Authors string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendAuthors (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Authors string

AjBool RETURN True on success

Input

str:

(Input)

Authors string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the Authors string of a citation

Availability

In release 6.4.0

Function ajSeqrefAppendComment

Append to the Comment string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendComment (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Comment string

AjBool RETURN True on success

Input

str:

(Input)

Comment string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the Comment string of a citation

Availability

In release 6.4.0

Function ajSeqrefAppendGroupname

Append to the group name string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendGroupname (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Group name string

AjBool RETURN True on success

Input

str:

(Input)

Group name string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the group name string of a citation

Availability

In release 6.4.0

Function ajSeqrefAppendLocation

Append to the location string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendLocation (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Location string

AjBool RETURN True on success

Input

str:

(Input)

Location string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the location string of a citation

Availability

In release 6.4.0

Function ajSeqrefAppendPosition

Append to the position string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendPosition (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Position string

AjBool RETURN True on success

Input

str:

(Input)

Position string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the position string of a citation

Availability

In release 6.4.0

Function ajSeqrefAppendTitle

Append to the title string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendTitle (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Title string

AjBool RETURN True on success

Input

str:

(Input)

Title string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the title string of a citation

Availability

In release 6.4.0

Function ajSeqrefAppendXref

Append to the Cross reference string of a citation

Synopsis

Prototype

AjBool ajSeqrefAppendXref (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Xref string

AjBool RETURN True on success

Input

str:

(Input)

Xref string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Append to the Cross reference string of a citation

Availability

In release 6.4.0

Function ajSeqrefFmtAuthorsEmbl

Return the Authors string of a citation in EMBL format

Synopsis

Prototype

AjBool ajSeqrefFmtAuthorsEmbl (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

Type Name Read/Write Description

const AjPSeqRef ref Input Sequence citation object

AjPStr* Pdest Output Authors string in EMBL format

AjBool RETURN True if author list exists

Input

ref:

(Input)

Sequence citation object

Output

Pdest:

(Output)

Authors string in EMBL format

Returns

AjBool:

True if author list exists

Description

Return the Authors string of a citation in EMBL format

Availability

In release 6.4.0

Function ajSeqrefFmtAuthorsGb

Return the Authors string of a citation in Genbank format

Synopsis

Prototype

AjBool ajSeqrefFmtAuthorsGb (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

Type Name Read/Write Description

const AjPSeqRef ref Input Sequence citation object

AjPStr* Pdest Output Authors string in Genbank format

AjBool RETURN True if author list exists

Input

ref:

(Input)

Sequence citation object

Output

Pdest:

(Output)

Authors string in Genbank format

Returns

AjBool:

True if author list exists

Description

Return the Authors string of a citation in Genbank format

Availability

In release 6.4.0

Function ajSeqrefFmtLocationEmbl

Return the location string of a citation in EMBL format

Synopsis

Prototype

AjBool ajSeqrefFmtLocationEmbl (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

Type Name Read/Write Description

const AjPSeqRef ref Input Sequence citation object

AjPStr* Pdest Output Authors string in EMBL format

AjBool RETURN True if author list exists

Input

ref:

(Input)

Sequence citation object

Output

Pdest:

(Output)

Authors string in EMBL format

Returns

AjBool:

True if author list exists

Description

Return the location string of a citation in EMBL format

Availability

In release 6.4.0

Function ajSeqrefFmtLocationGb

Return the location string of a citation in Genbank format

Synopsis

Prototype

AjBool ajSeqrefFmtLocationGb (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

Type Name Read/Write Description

const AjPSeqRef ref Input Sequence citation object

AjPStr* Pdest Output Authors string in Genbank format

AjBool RETURN True if author list exists

Input

ref:

(Input)

Sequence citation object

Output

Pdest:

(Output)

Authors string in Genbank format

Returns

AjBool:

True if author list exists

Description

Return the location string of a citation in Genbank format

Availability

In release 6.4.0

Function ajSeqrefFmtTitleGb

Return the title string of a citation in Genbank format

Synopsis

Prototype

AjBool ajSeqrefFmtTitleGb (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

Type Name Read/Write Description

const AjPSeqRef ref Input Sequence citation object

AjPStr* Pdest Output Authors string in Genbank format

AjBool RETURN True if author list exists

Input

ref:

(Input)

Sequence citation object

Output

Pdest:

(Output)

Authors string in Genbank format

Returns

AjBool:

True if author list exists

Description

Return the title string of a citation in Genbank format

Availability

In release 6.4.0

Function ajSeqrefSetAuthors

Set the Authors string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetAuthors (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Authors string

AjBool RETURN True on success

Input

str:

(Input)

Authors string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the Authors string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetComment

Set the Comment string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetComment (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Comment string

AjBool RETURN True on success

Input

str:

(Input)

Comment string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the Comment string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetGroupname

Set the group name string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetGroupname (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Groupname string

AjBool RETURN True on success

Input

str:

(Input)

Groupname string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the group name string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetLocation

Set the location string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetLocation (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Location string

AjBool RETURN True on success

Input

str:

(Input)

Location string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the location string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetLoctype

Set the location type of a citation

Synopsis

Prototype

AjBool ajSeqrefSetLoctype (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Location string

AjBool RETURN True on success

Input

str:

(Input)

Location string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the location type of a citation

Availability

In release 6.4.0

Function ajSeqrefSetPosition

Set the position string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetPosition (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input pPosition string

AjBool RETURN True on success

Input

str:

(Input)

pPosition string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the position string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetTitle

Set the title string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetTitle (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Title string

AjBool RETURN True on success

Input

str:

(Input)

Title string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the title string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetXref

Set the cross reference string of a citation

Synopsis

Prototype

AjBool ajSeqrefSetXref (
      AjPSeqRef ref,
      const AjPStr str
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

const AjPStr str Input Xref string

AjBool RETURN True on success

Input

str:

(Input)

Xref string

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Set the cross reference string of a citation

Availability

In release 6.4.0

Function ajSeqrefSetnumNumber

Sets the citation number

Synopsis

Prototype

AjBool ajSeqrefSetnumNumber (
      AjPSeqRef ref,
      ajuint num
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

ajuint num Input Citation number

AjBool RETURN True on success

Input

num:

(Input)

Citation number

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Sets the citation number

Availability

In release 6.4.0

Function ajSeqrefStandard

Standardise internal representation of a sequence reference

Synopsis

Prototype

AjBool ajSeqrefStandard (
      AjPSeqRef ref
);

Type Name Read/Write Description

AjPSeqRef ref Modify Sequence citation object

AjBool RETURN True on success

Input & Output

ref:

(Modify)

Sequence citation object

Returns

AjBool:

True on success

Description

Standardise internal representation of a sequence reference

Availability

In release 6.4.0

Datatype: AjPList

Reference list operations

Sections: Reference list operations element retrieval

Section: Reference list operations

Manipulating lists of sequence citations

Functions: ajSeqreflistClone

Function ajSeqreflistClone

Copy a list of citations to another list

Synopsis

Prototype

AjBool ajSeqreflistClone (
      const AjPList src,
      AjPList dest
);

Type Name Read/Write Description

const AjPList src Input Source list of citations

AjPList dest Output Destination list of citations

AjBool RETURN True on success

Input

src:

(Input)

Source list of citations

Output

dest:

(Output)

Destination list of citations

Returns

AjBool:

True on success

Description

Copy a list of citations to another list

Availability

In release 6.4.0

Section: element retrieval

These functions return contents of a list of sequence cross-reference objects.

Functions: ajSeqreflistGetXrefs

Function ajSeqreflistGetXrefs

Copy a cross-reference list

Synopsis

Prototype

ajuint ajSeqreflistGetXrefs (
      const AjPList src,
      AjPList* Plist
);

Type Name Read/Write Description

const AjPList src Input Source cross-reference list

AjPList* Plist Output Target list, created if it does not already exist

ajuint RETURN number of cross-references copied

Input

src:

(Input)

Source cross-reference list

Output

Plist:

(Output)

Target list, created if it does not already exist

Returns

ajuint:

number of cross-references copied

Description

Copy a cross-reference list

Availability

In release 6.4.0

Datatype: AjPStr

string tests

Sections: string tests

Section: string tests

Functions: ajSeqtestIsAccession ajSeqtestIsSeqversion

Function ajSeqtestIsAccession

Tests whether a string is a potential sequence accession number. The current definition is one or two alpha characters, then a possible underscore (for REFSEQ accessions), followed by a string of digits and a minimum length of 6.

Revised for new Swiss-Prot accession number format AnXXXn

Synopsis

Prototype

AjBool ajSeqtestIsAccession (
      const AjPStr str
);

Type Name Read/Write Description

const AjPStr str Input String to be tested

AjBool RETURN ajTrue if the string is a possible accession number.

Input

str:

(Input)

String to be tested

Returns

AjBool:

ajTrue if the string is a possible accession number.

Description

Revised for new Swiss-Prot accession number format AnXXXn

Availability

In release 6.4.0

Function ajSeqtestIsSeqversion

Tests whether a string is a potential sequence version number. The current definition is an accession number, followed by a dot and a number.

Revised for new Swiss-Prot accession number format AnXXXn Revised for REFSEQ accession number format NM_nnnnnn Revised for protein ID format XXXnnnnnn.nnn

Synopsis

Prototype

const AjPStr ajSeqtestIsSeqversion (
      const AjPStr str
);

Type Name Read/Write Description

const AjPStr str Input String to be tested

const AjPStr RETURN accession number part of the string if successful

Input

str:

(Input)

String to be tested

Returns

const AjPStr:

accession number part of the string if successful

Description

Tests whether a string is a potential sequence version number. The current definition is an accession number, followed by a dot and a number.

Revised for new Swiss-Prot accession number format AnXXXn Revised for REFSEQ accession number format NM_nnnnnn Revised for protein ID format XXXnnnnnn.nnn

Availability

In release 6.4.0

Section: string properties

Functions: ajSeqstrCalcMolwt ajSeqstrCountGaps

Function ajSeqstrCalcMolwt

Calculates the molecular weight of a protein sequence using average molecular weights

Synopsis

Prototype

float ajSeqstrCalcMolwt (
      const AjPStr seq
);

Type Name Read/Write Description

const AjPStr seq Input Sequence

float RETURN Molecular weight.

Input

seq:

(Input)

Sequence

Returns

float:

Molecular weight.

Description

Calculates the molecular weight of a protein sequence using average molecular weights

Availability

In release 6.4.0

Function ajSeqstrCountGaps

Complements but does not reverse a nucleotide sequence provided as a string.

Synopsis

Prototype

ajuint ajSeqstrCountGaps (
      const AjPStr seq
);

Type Name Read/Write Description

const AjPStr seq Input Sequence as a string.

ajuint RETURN Number of gap characters

Input

seq:

(Input)

Sequence as a string.

Returns

ajuint:

Number of gap characters

Description

Complements but does not reverse a nucleotide sequence provided as a string.

Availability

In release 6.4.0

Section: string processing

Functions: ajSeqstrComplement ajSeqstrReverse

Function ajSeqstrComplement

Complements but does not reverse a nucleotide sequence provided as a string.

Synopsis

Prototype

void ajSeqstrComplement (
      AjPStr* Pseq
);

Type Name Read/Write Description

AjPStr* Pseq Modify Sequence as a string.

void RETURN

Input & Output

Pseq:

(Modify)

Sequence as a string.

Returns

void:

No return value

Description

Complements but does not reverse a nucleotide sequence provided as a string.

Availability

In release 6.4.0

Function ajSeqstrReverse

Reverses and complements a nucleotide sequence provided as a string.

Synopsis

Prototype

void ajSeqstrReverse (
      AjPStr* Pseq
);

Type Name Read/Write Description

AjPStr* Pseq Modify Sequence as a string.

void RETURN

Input & Output

Pseq:

(Modify)

Sequence as a string.

Returns

void:

No return value

Description

Reverses and complements a nucleotide sequence provided as a string.

Availability

In release 6.4.0

Section: assignment

Assign values for sequence entry classes

Functions: ajSeqclsSetEmbl ajSeqclsSetGb

Function ajSeqclsSetEmbl

Sets the internal entry class for a sequence

Synopsis

Prototype

AjBool ajSeqclsSetEmbl (
      AjPStr* Pcls,
      const AjPStr clsembl
);

Type Name Read/Write Description

AjPStr* Pcls Modify Internal entry class name

const AjPStr clsembl Input EMBL database entry class

AjBool RETURN True if a known type

Input

clsembl:

(Input)

EMBL database entry class

Input & Output

Pcls:

(Modify)

Internal entry class name

Returns

AjBool:

True if a known type

Description

Sets the internal entry class for a sequence

Availability

In release 6.4.0

Function ajSeqclsSetGb

Sets the internal entry class for a sequence

Synopsis

Prototype

AjBool ajSeqclsSetGb (
      AjPStr* Pcls,
      const AjPStr clsgb
);

Type Name Read/Write Description

AjPStr* Pcls Modify Internal entry class name

const AjPStr clsgb Input Genbank database entry class

AjBool RETURN True if a known type

Input

clsgb:

(Input)

Genbank database entry class

Input & Output

Pcls:

(Modify)

Internal entry class name

Returns

AjBool:

True if a known type

Description

Sets the internal entry class for a sequence

Availability

In release 6.4.0

Section: retrieval

Return values for sequence entry class

Functions: ajSeqclsGetEmbl

Function ajSeqclsGetEmbl

Returns the EMBL entry class for a sequence

Synopsis

Prototype

const char* ajSeqclsGetEmbl (
      const AjPStr cls
);

Type Name Read/Write Description

const AjPStr cls Input Internal entry class name

const char* RETURN EMBL entry class name

Input

cls:

(Input)

Internal entry class name

Returns

const char*:

EMBL entry class name

Description

Returns the EMBL entry class for a sequence

Availability

In release 6.4.0

Section: assignment

Assign values for sequence entry division

Functions: ajSeqdivSetEmbl ajSeqdivSetGb

Function ajSeqdivSetEmbl

Sets the internal database division for a sequence

Synopsis

Prototype

AjBool ajSeqdivSetEmbl (
      AjPStr* Pdivi,
      const AjPStr divembl
);

Type Name Read/Write Description

AjPStr* Pdivi Modify Internal database division

const AjPStr divembl Input EMBL database division

AjBool RETURN True if a known type

Input

divembl:

(Input)

EMBL database division

Input & Output

Pdivi:

(Modify)

Internal database division

Returns

AjBool:

True if a known type

Description

Sets the internal database division for a sequence

Availability

In release 6.4.0

Function ajSeqdivSetGb

Sets the internal database division for a sequence

Synopsis

Prototype

AjBool ajSeqdivSetGb (
      AjPStr* Pdivi,
      const AjPStr divgb
);

Type Name Read/Write Description

AjPStr* Pdivi Modify Internal database division

const AjPStr divgb Input Genbank database division

AjBool RETURN True if a known type

Input

divgb:

(Input)

Genbank database division

Input & Output

Pdivi:

(Modify)

Internal database division

Returns

AjBool:

True if a known type

Description

Sets the internal database division for a sequence

Availability

In release 6.4.0

Section: retrieval

Return values for sequence entry division

Functions: ajSeqdivGetEmbl ajSeqdivGetGb

Function ajSeqdivGetEmbl

Returns the EMBL database division for a sequence

Synopsis

Prototype

const char* ajSeqdivGetEmbl (
      const AjPStr divi
);

Type Name Read/Write Description

const AjPStr divi Input Internal database division

const char* RETURN EMBL database division

Input

divi:

(Input)

Internal database division

Returns

const char*:

EMBL database division

Description

Returns the EMBL database division for a sequence

Availability

In release 6.4.0

Function ajSeqdivGetGb

Returns the Genbank database division for a sequence

Synopsis

Prototype

const char* ajSeqdivGetGb (
      const AjPStr divi
);

Type Name Read/Write Description

const AjPStr divi Input Internal database division

const char* RETURN Genbank database division

Input

divi:

(Input)

Internal database division

Returns

const char*:

Genbank database division

Description

Returns the Genbank database division for a sequence

Availability

In release 6.4.0

Section: assignment

Assign values for sequence entry molecule types

Functions: ajSeqmolSetEmbl ajSeqmolSetGb

Function ajSeqmolSetEmbl

Sets the internal molecule type for a sequence

Synopsis

Prototype

AjBool ajSeqmolSetEmbl (
      AjPStr* Pmol,
      const AjPStr molembl
);

Type Name Read/Write Description

AjPStr* Pmol Modify Sequence object

const AjPStr molembl Input Molecule type

AjBool RETURN True if a known type

Input

molembl:

(Input)

Molecule type

Input & Output

Pmol:

(Modify)

Sequence object

Returns

AjBool:

True if a known type

Description

Sets the internal molecule type for a sequence

Availability

In release 6.4.0

Function ajSeqmolSetGb

Sets the internal molecule type for a sequence

Synopsis

Prototype

AjBool ajSeqmolSetGb (
      AjPStr* Pmol,
      const AjPStr molgb
);

Type Name Read/Write Description

AjPStr* Pmol Modify Sequence object

const AjPStr molgb Input Molecule type

AjBool RETURN True if a known type

Input

molgb:

(Input)

Molecule type

Input & Output

Pmol:

(Modify)

Sequence object

Returns

AjBool:

True if a known type

Description

Sets the internal molecule type for a sequence

Availability

In release 6.4.0

Section: retrieval

Return values for sequence molecule type division

Functions: ajSeqmolGetEmbl ajSeqmolGetGb

Function ajSeqmolGetEmbl

Returns the EMBL molecule type for a sequence

Synopsis

Prototype

const char* ajSeqmolGetEmbl (
      const AjPStr mol
);

Type Name Read/Write Description

const AjPStr mol Input Internal molecule type

const char* RETURN EMBL molecule type

Input

mol:

(Input)

Internal molecule type

Returns

const char*:

EMBL molecule type

Description

Returns the EMBL molecule type for a sequence

Availability

In release 6.4.0

Function ajSeqmolGetGb

Returns the Genbank molecule type for a sequence

Synopsis

Prototype

const char* ajSeqmolGetGb (
      const AjPStr mol
);

Type Name Read/Write Description

const AjPStr mol Input Internal molecule type

const char* RETURN Genbank molecule type

Input

mol:

(Input)

Internal molecule type

Returns

const char*:

Genbank molecule type

Description

Returns the Genbank molecule type for a sequence

Availability

In release 6.4.0

Type	Name	Read/Write	Description
AjPSeqall*	Pseq	Delete	Sequence stream object reference
void		RETURN

Type	Name	Read/Write	Description
AjPSeqall	seq	Modify	Sequence stream object to be set.
ajint	pos1	Input	Start position. Negative values are from the end.
ajint	pos2	Input	End position. Negative values are from the end.
void		RETURN

Type	Name	Read/Write	Description
const AjPSeqall	seq	Input	Seqall object pointer.
ajlong		RETURN	Number of sequences read.

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object.
const AjPStr		RETURN	Name as a string.

Type	Name	Read/Write	Description
AjPSeqset	seq	Modify	Sequence set object to be set.
ajint		RETURN	Number of gaps inserted

Type	Name	Read/Write	Description
const char*	bases	Input	Allowed sequence characters.
AjPSeqCvt		RETURN	Conversion table.

Type	Name	Read/Write	Description
const AjPPStr	basearray	Input	Allowed sequence character strings (size specified by parameter n)
ajint	numbases	Input	Number of strings
AjPSeqCvt		RETURN	Conversion table.

Type	Name	Read/Write	Description
const AjPSeqCvt	cvt	Input	Conversion table
char	ch	Input	Sequence character
ajint		RETURN	Conversion code

Type	Name	Read/Write	Description
const AjPSeqDate	date	Input	Sequence date object
AjPSeqDate		RETURN	Empty sequence date object

Type	Name	Read/Write	Description
const AjPSeqDesc	desc	Input	Description object
AjPSeqDesc		RETURN	Copied description object

Type	Name	Read/Write	Description
const AjPList	src	Input	Source list of descriptions
AjPList	dest	Output	Destination list of descriptions
AjBool		RETURN	True on success

Type	Name	Read/Write	Description
const AjPSeqSubdesc	desc	Input	Sub-description object
AjPSeqSubdesc		RETURN	Copied sub-description object

Type	Name	Read/Write	Description
const AjPSeqGene	gene	Input	Gene object
AjPSeqGene		RETURN	Copied gene object

Type	Name	Read/Write	Description
const AjPSeqXref	xref	Input	Sequence cross-reference object
AjPSeqXref		RETURN	Copied sequence cross-reference object

Type	Name	Read/Write	Description
AjPSeqXref*	Pxref	Delete	Sequence cross-reference object
void		RETURN

Type	Name	Read/Write	Description
AjPList	list	Modify	Source list of cross-references
AjBool		RETURN	True on success

Type	Name	Read/Write	Description
const AjPSeqRef	ref	Input	Sequence citation object
AjPSeqRef		RETURN	Copied sequence citation object

Type	Name	Read/Write	Description
AjPStr*	Pcls	Modify	Internal entry class name
const AjPStr	clsembl	Input	EMBL database entry class
AjBool		RETURN	True if a known type

Type	Name	Read/Write	Description
AjPStr*	Pdivi	Modify	Internal database division
const AjPStr	divembl	Input	EMBL database division
AjBool		RETURN	True if a known type

Type	Name	Read/Write	Description
const AjPStr	divi	Input	Internal database division
const char*		RETURN	EMBL database division

ajseq.c

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Type	Name	Read/Write	Description
AjPStr*	Pmol	Modify	Sequence object
const AjPStr	molembl	Input	Molecule type
AjBool		RETURN	True if a known type