ajseq.c

Datatypes:

AjPSeq	Sequence
AjPSeqall	Sequence stream
AjPSeqset	Sequence set
AjPStr	sequence strings
AjPSeqCvt	sequence conversion
AjPSeqDate	sequence dates
AjPSeqDesc	sequence descriptions
AjPList	Description list operations
AjPSeqSubdesc	sequence sub-descriptions
AjPList	Description list operations
AjPSeqGene	gene names
AjPList	Reference list operations
AjPSeqXref	sequence citations
AjPList	Cross-reference list operations
AjPSeqRef	sequence citations
AjPList	Reference list operations
AjPSeqRange	Sequence ranges
AjPStr	string tests

Datatype: AjPSeq

Sections:

constructors	Constructors
destructors	Destructors
modifiers	Modifiers
process	Modifiers
element retrieval	General use
testing properties	General use
conversion	Derievd values
calculated properties	General use
exit	Miscellaneous
debug	Miscellaneous

AjPSeq: constructors

Functions:

ajSeqNew	Creates and initialises a sequence object.
ajSeqNewNameC	Creates and initialises a sequence object with a specified existing sequence as a char
ajSeqNewNameS	Creates and initialises a sequence object with a specified existing sequence as a string
ajSeqNewRangeC	Creates and initialises a sequence object with a specified existing sequence as a string, and provides offsets and direction.
ajSeqNewRangeS	Creates and initialises a sequence object with a specified existing sequence as a string, and provides offsets and direction.
ajSeqNewRefseq	Creates and initialises a sequence object with a specified existing reference sequence.
ajSeqNewRes	Creates and initialises a sequence object with a specified sequence length.
ajSeqNewSeq	Creates and initialises a sequence object with a specified existing sequence.

Function ajSeqNew

Prototype

AjPSeq ajSeqNew (
      void
);

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

From EMBOSS 1.0.0

Function ajSeqNewNameC

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.

From EMBOSS 4.0.0

Function ajSeqNewNameS

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.

From EMBOSS 4.0.0

Function ajSeqNewRangeC

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.

From EMBOSS 4.0.0

Function ajSeqNewRangeS

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.

From EMBOSS 4.0.0

Function ajSeqNewRefseq

Prototype

AjPSeq ajSeqNewRefseq (
      const AjPRefseq refseq
);

Type	Name	Read/Write	Description
const AjPRefseq	refseq	Input	Reference sequence object
AjPSeq		RETURN	New sequence object.

From EMBOSS 4.0.0

Function ajSeqNewRes

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.

From EMBOSS 4.0.0

Function ajSeqNewSeq

Prototype

AjPSeq ajSeqNewSeq (
      const AjPSeq seq
);

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

From EMBOSS 4.0.0

AjPSeq: destructors

Functions:

ajSeqDel	Deletes a sequence object.
ajSeqDelarray	Destructor for array of sequence objects

Function ajSeqDel

Prototype

void ajSeqDel (
      AjPSeq* Pseq
);

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

From EMBOSS 1.0.0

Function ajSeqDelarray

Prototype

void ajSeqDelarray (
      AjPSeq** PPseq
);

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

From EMBOSS 6.0.0

AjPSeq: modifiers

Functions:

ajSeqAddCmt	Adds a comment to a sequence object
ajSeqAddGene	Adds a gene to a sequence object
ajSeqAddHost	Adds a host organism to a sequence object
ajSeqAddKey	Adds a keyword to a sequence object
ajSeqAddRef	Adds a literature reference to a sequence object
ajSeqAddXref	Adds a cross-reference to a sequence object
ajSeqAssignAccC	Assigns the sequence accession number.
ajSeqAssignAccS	Assigns the sequence accession number.
ajSeqAssignDescC	Assigns a modified description to an existing AjPSeq sequence.
ajSeqAssignDescS	Assigns a modified description to an existing AjPSeq sequence.
ajSeqAssignEntryC	Assigns the sequence entryname.
ajSeqAssignEntryS	Assigns the sequence entryname.
ajSeqAssignFileC	Assigns the sequence filename.
ajSeqAssignFileS	Assigns the sequence file name.
ajSeqAssignFullC	Assigns the sequence name.
ajSeqAssignFullS	Assigns the sequence full name.
ajSeqAssignGiC	Assigns the GI version number.
ajSeqAssignGiS	Assigns the GI version number.
ajSeqAssignNameC	Assigns the sequence name.
ajSeqAssignNameS	Assigns the sequence name.
ajSeqAssignQualLen	Assigns base quality scores to an existing sequence.
ajSeqAssignSeqC	Assigns a modified sequence to an existing AjPSeq sequence.
ajSeqAssignSeqLenC	Assigns a modified sequence to an existing AjPSeq sequence.
ajSeqAssignSeqS	Assigns a modified sequence to an existing AjPSeq sequence.
ajSeqAssignSvC	Assigns the sequence version number.
ajSeqAssignSvS	Assigns the sequence version number.
ajSeqAssignUfoC	Assigns the sequence feature file name.
ajSeqAssignUfoS	Assigns the sequence feature file name.
ajSeqAssignUsaC	Assigns the sequence full name.
ajSeqAssignUsaS	Assigns the sequence full name.
ajSeqClear	Resets all data for a sequence object so that it can be reused.
ajSeqSetCircular	Sets a sequence to be circular
ajSeqSetName	Provides a unique (for this program run) name for a sequence.
ajSeqSetNameMulti	Provides a unique (for this program run) name for a sequence. If a name is generated, append a count
ajSeqSetOffsets	Sets the offsets for each end of a subsequence.
ajSeqSetRange	Sets the start and end positions for a sequence (not for a sequence set). Trim the sequence to convert to the subsequence.
ajSeqSetRangeRev	Sets the start and end positions for a sequence (not for a sequence set), and set the sequence to be reversed.
ajSeqSetUnique	Makes a sequence modifiable by making sure there is no duplicate copy of the sequence.
ajSeqTagRev	Adds a tag to the sequence description to note it has been reversed

Function ajSeqAddCmt

Prototype

void ajSeqAddCmt (
      AjPSeq seq,
      AjPStr str
);

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

From EMBOSS 6.2.0

Function ajSeqAddGene

Prototype

void ajSeqAddGene (
      AjPSeq seq,
      AjPSeqGene gene
);

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

From EMBOSS 6.2.0

Function ajSeqAddHost

Prototype

void ajSeqAddHost (
      AjPSeq seq,
      AjPStr str
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object.
AjPStr	str	Modify	Host organism swissprot formatted string
void		RETURN

From EMBOSS 6.6.0

Function ajSeqAddKey

Prototype

void ajSeqAddKey (
      AjPSeq seq,
      AjPStr str
);

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

From EMBOSS 6.2.0

Function ajSeqAddRef

Prototype

void ajSeqAddRef (
      AjPSeq seq,
      AjPSeqRef ref
);

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

From EMBOSS 6.2.0

Function ajSeqAddXref

Prototype

void ajSeqAddXref (
      AjPSeq seq,
      AjPSeqXref xref
);

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

From EMBOSS 6.2.0

Function ajSeqAssignAccC

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

From EMBOSS 4.0.0

Function ajSeqAssignAccS

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

From EMBOSS 4.0.0

Function ajSeqAssignDescC

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

From EMBOSS 4.0.0

Function ajSeqAssignDescS

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

From EMBOSS 4.0.0

Function ajSeqAssignEntryC

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

From EMBOSS 4.0.0

Function ajSeqAssignEntryS

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

From EMBOSS 4.0.0

Function ajSeqAssignFileC

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

From EMBOSS 4.0.0

Function ajSeqAssignFileS

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

From EMBOSS 4.0.0

Function ajSeqAssignFullC

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

From EMBOSS 4.0.0

Function ajSeqAssignFullS

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

From EMBOSS 4.0.0

Function ajSeqAssignGiC

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

From EMBOSS 4.0.0

Function ajSeqAssignGiS

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

From EMBOSS 4.0.0

Function ajSeqAssignNameC

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

From EMBOSS 4.0.0

Function ajSeqAssignNameS

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

From EMBOSS 4.0.0

Function ajSeqAssignQualLen

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

From EMBOSS 6.3.0

Function ajSeqAssignSeqC

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

From EMBOSS 4.0.0

Function ajSeqAssignSeqLenC

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

From EMBOSS 4.0.0

Function ajSeqAssignSeqS

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

From EMBOSS 4.0.0

Function ajSeqAssignSvC

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

From EMBOSS 4.0.0

Function ajSeqAssignSvS

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

From EMBOSS 4.0.0

Function ajSeqAssignUfoC

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

From EMBOSS 4.0.0

Function ajSeqAssignUfoS

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

From EMBOSS 4.0.0

Function ajSeqAssignUsaC

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

From EMBOSS 4.0.0

Function ajSeqAssignUsaS

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

From EMBOSS 4.0.0

Function ajSeqClear

Prototype

void ajSeqClear (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 1.0.0

Function ajSeqSetCircular

Prototype

void ajSeqSetCircular (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 6.5.0

Function ajSeqSetName

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

From EMBOSS 4.1.0

Function ajSeqSetNameMulti

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

From EMBOSS 4.1.0

Function ajSeqSetOffsets

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

From EMBOSS 3.0.0

Function ajSeqSetRange

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

From EMBOSS 1.0.0

Function ajSeqSetRangeRev

Prototype

void ajSeqSetRangeRev (
      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

From EMBOSS 4.0.0

Function ajSeqSetUnique

Prototype

void ajSeqSetUnique (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 4.1.0

Function ajSeqTagRev

Prototype

void ajSeqTagRev (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence object to be set.
void		RETURN

From EMBOSS 6.1.0

AjPSeq: process

Functions:

ajSeqComplement	Complements but does not reverse a nucleotide sequence.
ajSeqFmtLower	Converts a sequence to lower case.
ajSeqFmtUpper	Converts a sequence to upper case.
ajSeqGapFill	Fills a single sequence with gaps up to a specified length.
ajSeqGapStandard	Makes all gaps in a string use a standard gap character
ajSeqReverseDo	Reverses and complements a nucleotide sequence, unless it is already done.
ajSeqReverseForce	Reverses and complements a nucleotide sequence. Forces reversal to be done even if the sequence is flagged as already reversed.
ajSeqReverseOnly	Reverses but does not complement a nucleotide sequence.
ajSeqTrim	Trim a sequence using the Begin and Ends. Also reverse complements a nucleotide sequence if required.

Function ajSeqComplement

Prototype

void ajSeqComplement (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 4.1.0

Function ajSeqFmtLower

Prototype

void ajSeqFmtLower (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 4.0.0

Function ajSeqFmtUpper

Prototype

void ajSeqFmtUpper (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 4.0.0

Function ajSeqGapFill

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

From EMBOSS 4.1.0

Function ajSeqGapStandard

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

From EMBOSS 2.1.0

Function ajSeqReverseDo

Prototype

void ajSeqReverseDo (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 4.0.0

Function ajSeqReverseForce

Prototype

void ajSeqReverseForce (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 2.7.0

Function ajSeqReverseOnly

Prototype

void ajSeqReverseOnly (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence
void		RETURN

From EMBOSS 4.0.0

Function ajSeqTrim

Prototype

void ajSeqTrim (
      AjPSeq seq
);

Type	Name	Read/Write	Description
AjPSeq	seq	Modify	Sequence to be trimmed.
void		RETURN

From EMBOSS 1.0.0

AjPSeq: element retrieval

Functions:

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.
ajSeqGetAccS	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.
ajSeqGetBegin	Returns the sequence start position within the current stored sequence, or 1 if no start has been set.
ajSeqGetBeginTrue	Returns the sequence start position in the original sequence, which may have been trimmed.
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.
ajSeqGetDbS	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.
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.
ajSeqGetDescS	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.
ajSeqGetEnd	Returns the sequence end position, or the sequence length if no end has been set.
ajSeqGetEndTrue	Returns the sequence end position, or the sequence length if no end has been set.
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.
ajSeqGetEntryS	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.
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.
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.
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.
ajSeqGetGiS	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.
ajSeqGetLen	Returns the sequence length.
ajSeqGetLenTrimmed	Returns the sequence length after trimming begin and end positions
ajSeqGetLenTrue	Returns the length of the original sequence, including any gap characters.
ajSeqGetLenUngapped	Returns the sequence length excluding all gap characters.
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.
ajSeqGetNameS	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.
ajSeqGetOffend	Returns the sequence offend value. This is the number of positions removed from the original end.
ajSeqGetOffset	Returns the sequence offset from -sbegin originally.
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.
ajSeqGetRange	Returns the sequence range for a sequence.
ajSeqGetRev	Returns the sequence direction.
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.
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.
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.
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.
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.
ajSeqGetSvS	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.
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.
ajSeqGetTaxS	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.
ajSeqGetTaxid	Returns the numeric identifier of the sequence primary taxon (species). This is an identifier from the NCBI taxonomy
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.
ajSeqGetUsaS	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.
ajSeqGetXrefs	Returns the list of cross-references derived from the sequence

Function ajSeqGetAccC

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.

From EMBOSS 4.0.0

Function ajSeqGetAccS

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.

From EMBOSS 4.0.0

Function ajSeqGetBegin

Prototype

ajuint ajSeqGetBegin (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Start position.

From EMBOSS 4.0.0

Function ajSeqGetBeginTrue

Prototype

ajuint ajSeqGetBeginTrue (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Start position.

From EMBOSS 4.0.0

Function ajSeqGetDbC

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.

From EMBOSS 5.0.0

Function ajSeqGetDbS

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.

From EMBOSS 5.0.0

Function ajSeqGetDescC

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.

From EMBOSS 4.0.0

Function ajSeqGetDescS

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.

From EMBOSS 4.0.0

Function ajSeqGetEnd

Prototype

ajuint ajSeqGetEnd (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	End position.

From EMBOSS 4.0.0

Function ajSeqGetEndTrue

Prototype

ajuint ajSeqGetEndTrue (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	End position.

From EMBOSS 4.0.0

Function ajSeqGetEntryC

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.

From EMBOSS 4.0.0

Function ajSeqGetEntryS

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.

From EMBOSS 4.0.0

Function ajSeqGetFeat

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)

From EMBOSS 1.0.0

Function ajSeqGetFeatCopy

Prototype

AjPFeattable ajSeqGetFeatCopy (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object.
AjPFeattable		RETURN	feature table (if any)

From EMBOSS 4.0.0

Function ajSeqGetGiC

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.

From EMBOSS 4.0.0

Function ajSeqGetGiS

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.

From EMBOSS 4.0.0

Function ajSeqGetLen

Prototype

ajuint ajSeqGetLen (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Sequence length.

From EMBOSS 4.0.0

Function ajSeqGetLenTrimmed

Prototype

ajuint ajSeqGetLenTrimmed (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Sequence length.

From EMBOSS 6.1.0

Function ajSeqGetLenTrue

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.

From EMBOSS 4.0.0

Function ajSeqGetLenUngapped

Prototype

ajuint ajSeqGetLenUngapped (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Sequence length.

From EMBOSS 6.1.0

Function ajSeqGetNameC

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.

From EMBOSS 4.0.0

Function ajSeqGetNameS

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.

From EMBOSS 4.0.0

Function ajSeqGetOffend

Prototype

ajuint ajSeqGetOffend (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Sequence offend.

From EMBOSS 4.0.0

Function ajSeqGetOffset

Prototype

ajuint ajSeqGetOffset (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Sequence offset.

From EMBOSS 4.0.0

Function ajSeqGetQual

Prototype

const float* ajSeqGetQual (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence.
const float*		RETURN	Base quality scores.

From EMBOSS 6.3.0

Function ajSeqGetRange

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

From EMBOSS 1.0.0

Function ajSeqGetRev

Prototype

AjBool ajSeqGetRev (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
AjBool		RETURN	Sequence Direction.

From EMBOSS 4.0.0

Function ajSeqGetSeqC

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.

From EMBOSS 4.0.0

Function ajSeqGetSeqS

Prototype

const AjPStr ajSeqGetSeqS (
      const AjPSeq seq
);

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

From EMBOSS 4.0.0

Function ajSeqGetSeqCopyC

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.

From EMBOSS 4.0.0

Function ajSeqGetSeqCopyS

Prototype

AjPStr ajSeqGetSeqCopyS (
      const AjPSeq seq
);

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

From EMBOSS 4.0.0

Function ajSeqGetSvC

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.

From EMBOSS 4.0.0

Function ajSeqGetSvS

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.

From EMBOSS 4.0.0

Function ajSeqGetTaxC

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.

From EMBOSS 4.0.0

Function ajSeqGetTaxS

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.

From EMBOSS 4.0.0

Function ajSeqGetTaxid

Prototype

ajuint ajSeqGetTaxid (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object.
ajuint		RETURN	Taxon ID.

From EMBOSS 6.1.0

Function ajSeqGetUsaC

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.

From EMBOSS 4.0.0

Function ajSeqGetUsaS

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.

From EMBOSS 4.0.0

Function ajSeqGetXrefs

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

From EMBOSS 6.4.0

AjPSeq: testing properties

Functions:

ajSeqIsCircular	Returns true if a sequence is circular
ajSeqIsNuc	Tests whether a sequence is nucleotide.
ajSeqIsProt	Tests whether a sequence is protein.
ajSeqIsReversed	Returns whether the sequence has been reversed
ajSeqIsReversedTrue	Returns ajTrue if the sequence is reversed relative to the original sequence
ajSeqIsSpeciesBsubtilis	Tests whether a sequence is annotated as B. subtilis
ajSeqIsSpeciesHuman	Tests whether a sequence is annotated as human
ajSeqIsSpeciesMouse	Tests whether a sequence is annotated as mouse
ajSeqIsSpeciesYeast	Tests whether a sequence is annotated as yeast (S. cerevisiae)
ajSeqIsTaxon	Tests whether a sequence is annotated as from a specific taxon ID.
ajSeqIsTrimmed	Returns ajTrue if the sequence is already trimmed

Function ajSeqIsCircular

Prototype

AjBool ajSeqIsCircular (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a circular sequence

From EMBOSS 2.5.0

Function ajSeqIsNuc

Prototype

AjBool ajSeqIsNuc (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a nucleotide sequence.

From EMBOSS 1.0.0

Function ajSeqIsProt

Prototype

AjBool ajSeqIsProt (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a protein sequence.

From EMBOSS 1.0.0

Function ajSeqIsReversed

Prototype

AjBool ajSeqIsReversed (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
AjBool		RETURN	Sequence Direction.

From EMBOSS 3.0.0

Function ajSeqIsReversedTrue

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

From EMBOSS 4.0.0

Function ajSeqIsSpeciesBsubtilis

Prototype

AjBool ajSeqIsSpeciesBsubtilis (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a nucleotide sequence.

From EMBOSS 6.1.0

Function ajSeqIsSpeciesHuman

Prototype

AjBool ajSeqIsSpeciesHuman (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a nucleotide sequence.

From EMBOSS 6.1.0

Function ajSeqIsSpeciesMouse

Prototype

AjBool ajSeqIsSpeciesMouse (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a nucleotide sequence.

From EMBOSS 6.1.0

Function ajSeqIsSpeciesYeast

Prototype

AjBool ajSeqIsSpeciesYeast (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
AjBool		RETURN	ajTrue for a nucleotide sequence.

From EMBOSS 6.1.0

Function ajSeqIsTaxon

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.

From EMBOSS 6.1.0

Function ajSeqIsTrimmed

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

From EMBOSS 3.0.0

AjPSeq: conversion

Functions:

ajSeqConvertNum

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

Function ajSeqConvertNum

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.

From EMBOSS 4.1.0

AjPSeq: calculated properties

Functions:

ajSeqCalcCheckgcg	Calculates a GCG checksum for a sequence.
ajSeqCalcCount	Counts the numbers of A, C, G and T in a nucleotide sequence.
ajSeqCalcMolwt	Calculates the molecular weight of a protein sequence.
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.
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.
ajSeqCountGaps	Returns the number of gaps in a sequence (counting any possible gap character

Function ajSeqCalcCheckgcg

Prototype

ajint ajSeqCalcCheckgcg (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence.
ajint		RETURN	GCG checksum.

From EMBOSS 4.0.0

Function ajSeqCalcCount

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

From EMBOSS 4.0.0

Function ajSeqCalcMolwt

Prototype

float ajSeqCalcMolwt (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence
float		RETURN	Molecular weight.

From EMBOSS 4.0.0

Function ajSeqCalcTruepos

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.

From EMBOSS 4.0.0

Function ajSeqCalcTrueposMin

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.

From EMBOSS 4.0.0

Function ajSeqCountGaps

Prototype

ajuint ajSeqCountGaps (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence object
ajuint		RETURN	Number of gaps

From EMBOSS 4.1.0

AjPSeq: exit

Functions:

ajSeqExit

Cleans up sequence processing internal memory

Function ajSeqExit

Prototype

void ajSeqExit (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 4.0.0

AjPSeq: debug

Functions:

ajSeqTrace	Debug calls to trace the data in a sequence object.
ajSeqTraceTitle	Reports an AjPSeq object to debug output

Function ajSeqTrace

Prototype

void ajSeqTrace (
      const AjPSeq seq
);

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Sequence.
void		RETURN

From EMBOSS 1.0.0

Function ajSeqTraceTitle

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

From EMBOSS 4.1.0

Datatype: AjPSeqall

Sections:

Sequence Stream Constructors	Constructors
destructors	Destructors
modifiers	Modifiers
casts	Casts

AjPSeqall: Sequence Stream Constructors

Functions:

ajSeqallNew

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

Function ajSeqallNew

Prototype

AjPSeqall ajSeqallNew (
      void
);

Type	Name	Read/Write	Description
AjPSeqall		RETURN	New sequence stream object.

From EMBOSS 1.0.0

AjPSeqall: destructors

Functions:

ajSeqallDel

Destructor for sequence stream objects

Function ajSeqallDel

Prototype

void ajSeqallDel (
      AjPSeqall* Pseq
);

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

From EMBOSS 2.0.0

AjPSeqall: modifiers

Functions:

ajSeqallClear	Resets all data internals for a sequence stream object when input has been read, but leaves statistics for reporting.
ajSeqallClearStats	Resets all data for a sequence stream object so that it can be reused, including statistics.
ajSeqallSetRange	Sets the start and end positions for a sequence stream.
ajSeqallSetRangeRev	Sets the start and end positions for a sequence stream, and set the sequences to be reversed.

Function ajSeqallClear

Prototype

void ajSeqallClear (
      AjPSeqall seq
);

Type	Name	Read/Write	Description
AjPSeqall	seq	Modify	Sequence stream
void		RETURN

From EMBOSS 2.7.0

Function ajSeqallClearStats

Prototype

void ajSeqallClearStats (
      AjPSeqall seq
);

Type	Name	Read/Write	Description
AjPSeqall	seq	Modify	Sequence stream
void		RETURN

From EMBOSS 6.1.0

Function ajSeqallSetRange

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

From EMBOSS 1.0.0

Function ajSeqallSetRangeRev

Prototype

void ajSeqallSetRangeRev (
      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

From EMBOSS 4.0.0

AjPSeqall: casts

Functions:

ajSeqallGetCount	Returns the number of sequences read by a seqall object
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.
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.
ajSeqallGetTotlength	Returns the total length of sequences read by a seqall object
ajSeqallGetUsa	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.
ajSeqallGetseqBegin	Returns the sequence stream start position, or 1 if no start has been set.
ajSeqallGetseqEnd	Returns the sequence stream end position, or the sequence length if no end has been set.
ajSeqallGetseqLen	Returns the length of a sequence stream, which is the length of the latest sequence read.
ajSeqallGetseqName	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.
ajSeqallGetseqRange	Returns the sequence range for a sequence stream

Function ajSeqallGetCount

Prototype

ajlong ajSeqallGetCount (
      const AjPSeqall seq
);

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

From EMBOSS 6.1.0

Function ajSeqallGetFilename

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.

From EMBOSS 4.0.0

Function ajSeqallGetName

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.

From EMBOSS 1.0.0

Function ajSeqallGetTotlength

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.

From EMBOSS 6.1.0

Function ajSeqallGetUsa

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.

From EMBOSS 1.8.0

Function ajSeqallGetseqBegin

Prototype

ajint ajSeqallGetseqBegin (
      const AjPSeqall seq
);

Type	Name	Read/Write	Description
const AjPSeqall	seq	Input	Sequence stream object
ajint		RETURN	Start position.

From EMBOSS 4.1.0

Function ajSeqallGetseqEnd

Prototype

ajint ajSeqallGetseqEnd (
      const AjPSeqall seq
);

Type	Name	Read/Write	Description
const AjPSeqall	seq	Input	Sequence stream object
ajint		RETURN	Start position.

From EMBOSS 4.1.0

Function ajSeqallGetseqLen

Prototype

ajint ajSeqallGetseqLen (
      const AjPSeqall seq
);

Type	Name	Read/Write	Description
const AjPSeqall	seq	Input	Sequence stream object
ajint		RETURN	sequence length.

From EMBOSS 4.1.0

Function ajSeqallGetseqName

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.

From EMBOSS 4.1.0

Function ajSeqallGetseqRange

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

From EMBOSS 4.1.0

Datatype: AjPSeqset

Sections:

constructors	Constructors
destructors	Destructors
casts	Casts
modifiers	Modifiers
element assignment	Modifiers
casts	Casts
testing properties	Casts

AjPSeqset: constructors

Functions:

ajSeqsetNew

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

Function ajSeqsetNew

Prototype

AjPSeqset ajSeqsetNew (
      void
);

Type	Name	Read/Write	Description
AjPSeqset		RETURN	New sequence set object.

From EMBOSS 1.0.0

AjPSeqset: destructors

Functions:

ajSeqsetDel	Destructor for sequence set objects
ajSeqsetDelarray	Destructor for array of sequence set objects

Function ajSeqsetDel

Prototype

void ajSeqsetDel (
      AjPSeqset* Pseq
);

Type	Name	Read/Write	Description
AjPSeqset*	Pseq	Delete	Sequence set object reference
void		RETURN

From EMBOSS 2.1.0

Function ajSeqsetDelarray

Prototype

void ajSeqsetDelarray (
      AjPSeqset** PPseq
);

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

From EMBOSS 4.0.0

AjPSeqset: casts

Functions:

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.
ajSeqsetGetFormat	Returns the sequence format for a sequence set
ajSeqsetGetOffend	Returns the sequence set offend value. This is the number of positions removed from the original end.
ajSeqsetGetOffset	Returns the sequence set offset value. This is the number of positions removed from the original end.
ajSeqsetGetRange	Returns the sequence range for a sequence set
ajSeqsetGetTotlength	Returns the total number of bases or residues in a sequence set, ignoring any gap characters in aligned sequences.
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.

Function ajSeqsetGetFilename

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.

From EMBOSS 4.0.0

Function ajSeqsetGetFormat

Prototype

const AjPStr ajSeqsetGetFormat (
      const AjPSeqset seq
);

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

From EMBOSS 2.0.1

Function ajSeqsetGetOffend

Prototype

ajint ajSeqsetGetOffend (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object
ajint		RETURN	Sequence offend.

From EMBOSS 4.1.0

Function ajSeqsetGetOffset

Prototype

ajint ajSeqsetGetOffset (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object
ajint		RETURN	Sequence offset.

From EMBOSS 4.1.0

Function ajSeqsetGetRange

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

From EMBOSS 1.0.0

Function ajSeqsetGetTotlength

Prototype

ajint ajSeqsetGetTotlength (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object.
ajint		RETURN	Total ungapped length

From EMBOSS 6.1.0

Function ajSeqsetGetUsa

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.

From EMBOSS 2.1.0

AjPSeqset: modifiers

Functions:

ajSeqsetClear	Reset a sequence set object
ajSeqsetFill	Fills a sequence set with gaps at the ends of any shorter sequences.
ajSeqsetFmtLower	Converts all sequences in a set to lower case.
ajSeqsetFmtUpper	Converts all sequences in a set to upper case.
ajSeqsetReverse	Reverse complements all sequences in a sequence set.
ajSeqsetSortLen	Sorts a sequence set by sequence length
ajSeqsetTrim	Trims a sequence set to start and end positions

Function ajSeqsetClear

Prototype

void ajSeqsetClear (
      AjPSeqset seq
);

Type	Name	Read/Write	Description
AjPSeqset	seq	Modify	Sequence set object reference
void		RETURN

From EMBOSS 6.5.0

Function ajSeqsetFill

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

From EMBOSS 1.0.0

Function ajSeqsetFmtLower

Prototype

void ajSeqsetFmtLower (
      AjPSeqset seq
);

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

From EMBOSS 4.1.0

Function ajSeqsetFmtUpper

Prototype

void ajSeqsetFmtUpper (
      AjPSeqset seq
);

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

From EMBOSS 4.1.0

Function ajSeqsetReverse

Prototype

void ajSeqsetReverse (
      AjPSeqset seq
);

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

From EMBOSS 1.0.0

Function ajSeqsetSortLen

Prototype

void ajSeqsetSortLen (
      AjPSeqset seq
);

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

From EMBOSS 6.1.0

Function ajSeqsetTrim

Prototype

void ajSeqsetTrim (
      AjPSeqset seq
);

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

From EMBOSS 2.9.0

AjPSeqset: element assignment

Functions:

ajSeqsetSetRange

Sets the start and end positions for a sequence set.

Function ajSeqsetSetRange

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

From EMBOSS 1.0.0

AjPSeqset: casts

Functions:

ajSeqsetGetBegin	Returns the sequence set start position, or 1 if no start has been set.
ajSeqsetGetEnd	Returns the sequence set end position, or the sequence length if no end has been set.
ajSeqsetGetLen	Returns the length of a sequence set, which is the maximum sequence length in the set.
ajSeqsetGetNameC	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.
ajSeqsetGetNameS	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.
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.
ajSeqsetGetSize	Returns the number of sequences in a sequence set
ajSeqsetGetTotweight	Returns the weight of all sequences in a sequence set
ajSeqsetGetseqAccC	Returns the accession number of a sequence in a sequence set
ajSeqsetGetseqAccS	Returns the accession number of a sequence in a sequence set
ajSeqsetGetseqNameC	Returns the name of a sequence in a sequence set
ajSeqsetGetseqNameS	Returns the name of a sequence in a sequence set
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.
ajSeqsetGetseqSeqC	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.
ajSeqsetGetseqSeqS	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.
ajSeqsetGetseqWeight	Returns the weight of a sequence in a sequence set

Function ajSeqsetGetBegin

Prototype

ajuint ajSeqsetGetBegin (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object
ajuint		RETURN	Start position.

From EMBOSS 4.1.0

Function ajSeqsetGetEnd

Prototype

ajuint ajSeqsetGetEnd (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object
ajuint		RETURN	Start position.

From EMBOSS 4.1.0

Function ajSeqsetGetLen

Prototype

ajuint ajSeqsetGetLen (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object
ajuint		RETURN	sequence set length.

From EMBOSS 4.1.0

Function ajSeqsetGetNameC

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.

From EMBOSS 4.1.0

Function ajSeqsetGetNameS

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.

From EMBOSS 4.1.0

Function ajSeqsetGetSeqarray

Prototype

AjPSeq* ajSeqsetGetSeqarray (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object.
AjPSeq*		RETURN	Sequence object.

From EMBOSS 4.1.0

Function ajSeqsetGetSize

Prototype

ajuint ajSeqsetGetSize (
      const AjPSeqset seq
);

Type	Name	Read/Write	Description
const AjPSeqset	seq	Input	Sequence set object
ajuint		RETURN	sequence set size.

From EMBOSS 4.1.0

Function ajSeqsetGetTotweight

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqAccC

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqAccS

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqNameC

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqNameS

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqSeq

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqSeqC

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqSeqS

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.

From EMBOSS 4.1.0

Function ajSeqsetGetseqWeight

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.

From EMBOSS 4.1.0

AjPSeqset: testing properties

Functions:

ajSeqsetIsDna	Tests whether a sequence set is DNA.
ajSeqsetIsNuc	Tests whether a sequence set is nucleotide.
ajSeqsetIsProt	Tests whether a sequence set is protein.
ajSeqsetIsRna	Tests whether a sequence set is RNA.

Function ajSeqsetIsDna

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.

From EMBOSS 2.3.0

Function ajSeqsetIsNuc

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.

From EMBOSS 1.0.0

Function ajSeqsetIsProt

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.

From EMBOSS 1.0.0

Function ajSeqsetIsRna

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.

From EMBOSS 2.0.1

Datatype: AjPStr

Sections:

conversion

Derievd values

AjPStr: conversion

Functions:

ajSeqstrConvertNum

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

Function ajSeqstrConvertNum

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.

From EMBOSS 4.1.0

Datatype: AjPSeqCvt

Sections:

Sequence Conversion Functions	Miscellaneous
constructors	Constructors
Sequence Destructors	Destructors
element retrieval	General use

AjPSeqCvt: Sequence Conversion Functions

Functions:

ajSeqcvtTrace

Traces a conversion table with debug calls.

Function ajSeqcvtTrace

Prototype

void ajSeqcvtTrace (
      const AjPSeqCvt cvt
);

Type	Name	Read/Write	Description
const AjPSeqCvt	cvt	Input	Conversion table.
void		RETURN

From EMBOSS 4.1.0

AjPSeqCvt: constructors

Functions:

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.
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.
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.
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.
ajSeqcvtNewStrAsym	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. For use with asymmetrical matrices.

Function ajSeqcvtNewC

Prototype

AjPSeqCvt ajSeqcvtNewC (
      const char* bases
);

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

From EMBOSS 4.1.0

Function ajSeqcvtNewEndC

Prototype

AjPSeqCvt ajSeqcvtNewEndC (
      const char* bases
);

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

From EMBOSS 4.1.0

Function ajSeqcvtNewNumberC

Prototype

AjPSeqCvt ajSeqcvtNewNumberC (
      const char* bases
);

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

From EMBOSS 4.1.0

Function ajSeqcvtNewStr

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.

From EMBOSS 4.1.0

Function ajSeqcvtNewStrAsym

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.

From EMBOSS 4.1.0

AjPSeqCvt: Sequence Destructors

Functions:

ajSeqcvtDel

Delete a conversion table

Function ajSeqcvtDel

Prototype

void ajSeqcvtDel (
      AjPSeqCvt* Pcvt
);

Type	Name	Read/Write	Description
AjPSeqCvt*	Pcvt	Output	Conversion table reference
void		RETURN

From EMBOSS 4.1.0

AjPSeqCvt: element retrieval

Functions:

ajSeqcvtGetCodeK	Returns the integer code corresponding to a sequence character in a conversion table
ajSeqcvtGetCodeS	Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).
ajSeqcvtGetCodeAsymS	Returns the integer code corresponding to a sequence character string in a conversion table (for columns in asymmetrical matrices).
ajSeqcvtGetCodeAsymrowS	Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).
ajSeqcvtGetLen	Returns the length of a conversion table string (number of sequence characters explicitly included)

Function ajSeqcvtGetCodeK

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

From EMBOSS 4.1.0

Function ajSeqcvtGetCodeS

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

From EMBOSS 4.1.0

Function ajSeqcvtGetCodeAsymS

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

From EMBOSS 4.1.0

Function ajSeqcvtGetCodeAsymrowS

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

From EMBOSS 6.3.0

Function ajSeqcvtGetLen

Prototype

ajuint ajSeqcvtGetLen (
      const AjPSeqCvt cvt
);

Type	Name	Read/Write	Description
const AjPSeqCvt	cvt	Input	Conversion table
ajuint		RETURN	Length

From EMBOSS 4.1.0

Datatype: AjPSeqDate

Sections:

sequence date constructors	Constructors
destructors	Destructors
tests	General use
modifiers	Modifiers

AjPSeqDate: sequence date constructors

Functions:

ajSeqdateNew	Constructor for empty sequence date object
ajSeqdateNewDate	Constructor for copy of a sequence date object

Function ajSeqdateNew

Prototype

AjPSeqDate ajSeqdateNew (
      void
);

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

From EMBOSS 5.0.0

Function ajSeqdateNewDate

Prototype

AjPSeqDate ajSeqdateNewDate (
      const AjPSeqDate date
);

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

From EMBOSS 5.0.0

AjPSeqDate: destructors

Functions:

ajSeqdateDel

Deletes a sequence date object.

Function ajSeqdateDel

Prototype

void ajSeqdateDel (
      AjPSeqDate* Pdate
);

Type	Name	Read/Write	Description
AjPSeqDate*	Pdate	Delete	Sequence date object
void		RETURN

From EMBOSS 5.0.0

AjPSeqDate: tests

Functions:

ajSeqdateExists

Returns true if a sequence has a creation or modification date defined

Function ajSeqdateExists

Prototype

AjBool ajSeqdateExists (
      const AjPSeqDate date
);

Type	Name	Read/Write	Description
const AjPSeqDate	date	Input	Sequence date
AjBool		RETURN	ajTrue if date(s) are defined

From EMBOSS 6.6.0

AjPSeqDate: modifiers

Functions:

ajSeqdateClear	Resets all data for a sequence date object.
ajSeqdateSetCreateS	Set the sequence creation date
ajSeqdateSetModifyS	Set the entry modification date
ajSeqdateSetModseqS	Set the sequence modification date

Function ajSeqdateClear

Prototype

void ajSeqdateClear (
      AjPSeqDate date
);

Type	Name	Read/Write	Description
AjPSeqDate	date	Modify	Sequence date object
void		RETURN

From EMBOSS 6.1.0

Function ajSeqdateSetCreateS

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

From EMBOSS 5.0.0

Function ajSeqdateSetModifyS

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

From EMBOSS 5.0.0

Function ajSeqdateSetModseqS

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

From EMBOSS 5.0.0

Datatype: AjPSeqDesc

Sections:

descriptions constructors	Constructors
destructors	Destructors
modifiers	Modifiers

AjPSeqDesc: descriptions constructors

Functions:

ajSeqdescNew	Constructor for empty description object
ajSeqdescNewDesc	Constructor for copy of a description object

Function ajSeqdescNew

Prototype

AjPSeqDesc ajSeqdescNew (
      void
);

Type	Name	Read/Write	Description
AjPSeqDesc		RETURN	Empty sequence description object

From EMBOSS 6.1.0

Function ajSeqdescNewDesc

Prototype

AjPSeqDesc ajSeqdescNewDesc (
      const AjPSeqDesc desc
);

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

From EMBOSS 6.1.0

AjPSeqDesc: destructors

Functions:

ajSeqdescDel

Deletes a description object.

Function ajSeqdescDel

Prototype

void ajSeqdescDel (
      AjPSeqDesc* Pdesc
);

Type	Name	Read/Write	Description
AjPSeqDesc*	Pdesc	Delete	Description object
void		RETURN

From EMBOSS 6.1.0

AjPSeqDesc: modifiers

Functions:

ajSeqdescAppendName	Append to the name of a description
ajSeqdescClear	Resets data for a description object.
ajSeqdescSetName	Set the name of a description object

Function ajSeqdescAppendName

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

From EMBOSS 6.1.0

Function ajSeqdescClear

Prototype

void ajSeqdescClear (
      AjPSeqDesc desc
);

Type	Name	Read/Write	Description
AjPSeqDesc	desc	Modify	Description object
void		RETURN

From EMBOSS 6.1.0

Function ajSeqdescSetName

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

From EMBOSS 6.1.0

Datatype: AjPList

Sections:

Description list operations

General use

AjPList: Description list operations

Functions:

ajSeqdesclistClone

Copy a list of genes to another list

Function ajSeqdesclistClone

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

From EMBOSS 6.1.0

Datatype: AjPSeqSubdesc

Sections:

sub-descriptions constructors	Constructors
destructors	Destructors
modifiers	Modifiers

AjPSeqSubdesc: sub-descriptions constructors

Functions:

ajSeqsubdescNew	Constructor for empty sub-description object
ajSeqsubdescNewSubdesc	Constructor for copy of a sub-description object

Function ajSeqsubdescNew

Prototype

AjPSeqSubdesc ajSeqsubdescNew (
      void
);

Type	Name	Read/Write	Description
AjPSeqSubdesc		RETURN	Empty sequence sub-description object

From EMBOSS 6.1.0

Function ajSeqsubdescNewSubdesc

Prototype

AjPSeqSubdesc ajSeqsubdescNewSubdesc (
      const AjPSeqSubdesc desc
);

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

From EMBOSS 6.1.0

AjPSeqSubdesc: destructors

Functions:

ajSeqsubdescDel

Deletes a sub-description object.

Function ajSeqsubdescDel

Prototype

void ajSeqsubdescDel (
      AjPSeqSubdesc* Pdesc
);

Type	Name	Read/Write	Description
AjPSeqSubdesc*	Pdesc	Delete	Sub-description object
void		RETURN

From EMBOSS 6.1.0

AjPSeqSubdesc: modifiers

Functions:

ajSeqsubdescAppendName	Append to the name of a description
ajSeqsubdescClear	Resets data for a sub-description object.
ajSeqsubdescSetName	Set the name of a sub-description object

Function ajSeqsubdescAppendName

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

From EMBOSS 6.1.0

Function ajSeqsubdescClear

Prototype

void ajSeqsubdescClear (
      AjPSeqSubdesc desc
);

Type	Name	Read/Write	Description
AjPSeqSubdesc	desc	Modify	Sub-description object
void		RETURN

From EMBOSS 6.1.0

Function ajSeqsubdescSetName

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

From EMBOSS 6.1.0

Datatype: AjPList

Sections:

Description list operations

General use

AjPList: Description list operations

Functions:

ajSeqsubdesclistClone

Copy a list of sub-descriptions to another list

Function ajSeqsubdesclistClone

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

From EMBOSS 6.1.0

Datatype: AjPSeqGene

Sections:

gene names constructors	Constructors
destructors	Destructors
modifiers	Modifiers

AjPSeqGene: gene names constructors

Functions:

ajSeqgeneNew	Constructor for empty gene object
ajSeqgeneNewGene	Constructor for copy of a gene object
ajSeqgeneNewName	Constructor for gene with given name

Function ajSeqgeneNew

Prototype

AjPSeqGene ajSeqgeneNew (
      void
);

Type	Name	Read/Write	Description
AjPSeqGene		RETURN	Empty sequence gene object

From EMBOSS 6.1.0

Function ajSeqgeneNewGene

Prototype

AjPSeqGene ajSeqgeneNewGene (
      const AjPSeqGene gene
);

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

From EMBOSS 6.1.0

Function ajSeqgeneNewName

Prototype

AjPSeqGene ajSeqgeneNewName (
      const AjPStr str
);

Type	Name	Read/Write	Description
const AjPStr	str	Input	Gene name
AjPSeqGene		RETURN	New gene object

From EMBOSS 6.1.0

AjPSeqGene: destructors

Functions:

ajSeqgeneDel

Deletes a gene object.

Function ajSeqgeneDel

Prototype

void ajSeqgeneDel (
      AjPSeqGene* Pgene
);

Type	Name	Read/Write	Description
AjPSeqGene*	Pgene	Delete	Gene object
void		RETURN

From EMBOSS 6.1.0

AjPSeqGene: modifiers

Functions:

ajSeqgeneAppendName	Append to the name of a gene
ajSeqgeneAppendOln	Append to ordered locus names of a gene
ajSeqgeneAppendOrf	Append to the ORF name of a gene
ajSeqgeneAppendSynonyms	Append to the name of a gene
ajSeqgeneSetName	Set the name of a gene
ajSeqgeneSetOln	Set the ordered locus names of a gene
ajSeqgeneSetOrf	Set the ORF name of a gene
ajSeqgeneSetSynonyms	Set the name of a gene