ajseqread.c

Section: Sequence Input Constructors

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

Functions:

ajSeqinNew Creates a new sequence input object.

Function ajSeqinNew

Creates a new sequence input object.

Prototype

AjPSeqin ajSeqinNew (
      void
);

Type Name Read/Write Description

AjPSeqin RETURN New sequence input object.

Type	Name	Read/Write	Description
`AjPSeqin`		RETURN	New sequence input object.

From EMBOSS 1.0.0

Section: Sequence Input Destructors

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

Functions:

ajSeqinDel Deletes a sequence input object.

Function ajSeqinDel

Deletes a sequence input object.

Prototype

void ajSeqinDel (
      AjPSeqin* pthis
);

Type Name Read/Write Description

AjPSeqin* pthis Delete Sequence input

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin*`	`pthis`	Delete	Sequence input
`void`		RETURN

From EMBOSS 1.0.0

Section: Sequence Input Modifiers

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

Functions:

ajSeqinUsa Creates or resets a sequence input object using a new Universal Sequence Address

ajSeqinSetNuc Sets the type to be forced as nucleic for a sequence input object

ajSeqinSetProt Sets the type to be forced as protein for a sequence input object

ajSeqinSetRange Sets the start and end positions for a sequence input object

Function ajSeqinUsa

Creates or resets a sequence input object using a new Universal Sequence Address

Prototype

void ajSeqinUsa (
      AjPSeqin* pthis,
      const AjPStr Usa
);

Type Name Read/Write Description

AjPSeqin* pthis Modify Sequence input object.

const AjPStr Usa Input USA

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin*`	`pthis`	Modify	Sequence input object.
`const AjPStr`	`Usa`	Input	USA
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqinSetNuc

Sets the type to be forced as nucleic for a sequence input object

Prototype

void ajSeqinSetNuc (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Sequence input object to be set.

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Sequence input object to be set.
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqinSetProt

Sets the type to be forced as protein for a sequence input object

Prototype

void ajSeqinSetProt (
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqin seqin Modify Sequence input object to be set.

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Sequence input object to be set.
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqinSetRange

Sets the start and end positions for a sequence input object

Prototype

void ajSeqinSetRange (
      AjPSeqin seqin,
      ajint ibegin,
      ajint iend
);

Type Name Read/Write Description

AjPSeqin seqin Modify Sequence input object to be set.

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

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

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`seqin`	Modify	Sequence input object to be set.
`ajint`	`ibegin`	Input	Start position. Negative values are from the end.
`ajint`	`iend`	Input	End position. Negative values are from the end.
`void`		RETURN

From EMBOSS 1.0.0

Section: Sequence Input Operators

These functions use the contents of a sequence input object but do not make any changes.

Functions:

ajSeqAllRead Parse a USA Uniform Sequence Address into format, access, file and entry

ajSeqallFile Parse a USA Uniform Sequence Address

ajSeqallNext Reads the next sequence into a sequence stream. For the first call this simply returns the sequence already loaded. For later calls a new sequence is read.

ajSeqinClearPos Clears a Sequence input object position information as possibly read from a USA that included the begin, end and direction

ajSeqinClear Clears a Sequence input object back to "as new" condition, except for the USA list and the features setting which must be preserved.

Function ajSeqAllRead

Parse a USA Uniform Sequence Address into format, access, file and entry

Prototype

AjBool ajSeqAllRead (
      AjPSeq thys,
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeq thys Output Sequence returned.

AjPSeqin seqin Modify Sequence input definitions

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Output	Sequence returned.
`AjPSeqin`	`seqin`	Modify	Sequence input definitions
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 1.0.0

Function ajSeqallFile

Parse a USA Uniform Sequence Address

Prototype

AjPSeqall ajSeqallFile (
      const AjPStr usa
);

Type Name Read/Write Description

const AjPStr usa Input sequence usa.

AjPSeqall RETURN seqall object

Type	Name	Read/Write	Description
`const AjPStr`	`usa`	Input	sequence usa.
`AjPSeqall`		RETURN	seqall object

From EMBOSS 1.13.0

Function ajSeqallNext

Reads the next sequence into a sequence stream. For the first call this simply returns the sequence already loaded. For later calls a new sequence is read.

Prototype

AjBool ajSeqallNext (
      AjPSeqall seqall,
      AjPSeq* retseq
);

Type Name Read/Write Description

AjPSeqall seqall Modify Sequence stream

AjPSeq* retseq Output Sequence

AjBool RETURN ajTrue if a sequence was refound. ajFalse when all is done.

Type	Name	Read/Write	Description
`AjPSeqall`	`seqall`	Modify	Sequence stream
`AjPSeq*`	`retseq`	Output	Sequence
`AjBool`		RETURN	ajTrue if a sequence was refound. ajFalse when all is done.

From EMBOSS 1.0.0

Function ajSeqinClearPos

Clears a Sequence input object position information as possibly read from a USA that included the begin, end and direction

Prototype

void ajSeqinClearPos (
      AjPSeqin thys
);

Type Name Read/Write Description

AjPSeqin thys Modify Sequence input

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`thys`	Modify	Sequence input
`void`		RETURN

From EMBOSS 2.9.0

Function ajSeqinClear

Clears a Sequence input object back to "as new" condition, except for the USA list and the features setting which must be preserved.

Prototype

void ajSeqinClear (
      AjPSeqin thys
);

Type Name Read/Write Description

AjPSeqin thys Output Sequence input

void RETURN

Type	Name	Read/Write	Description
`AjPSeqin`	`thys`	Output	Sequence input
`void`		RETURN

From EMBOSS 1.0.0

Section: Sequence inputs

These functions read the sequence provided by the first argument

Functions:

ajSeqRead If the file is not yet open, calls seqinUsaProcess to convert the USA into an open file stream.

Function ajSeqRead

If the file is not yet open, calls seqinUsaProcess to convert the USA into an open file stream.

Prototype

AjBool ajSeqRead (
      AjPSeq thys,
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeq thys Output Sequence returned.

AjPSeqin seqin Modify Sequence input definitions

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Output	Sequence returned.
`AjPSeqin`	`seqin`	Modify	Sequence input definitions
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 1.0.0

Section: Sequence Set Inputs

These functions read the sequence set object provided as the first argument.

Functions:

ajSeqsetRead Parse a USA Uniform Sequence Address into format, access, file and entry

ajSeqsetallRead Parse a USA Uniform Sequence Address into format, access, file and entry

ajSeqsetFromList Builds a sequence set from a list of sequences

ajSeqsetFromPair Builds a sequence set from a pair of sequences

ajSeqsetApp Adds a sequence to a sequence set

ajSeqPrintInFormat Reports the internal data structures

ajSeqPrintbookInFormat Reports the internal data structures as a Docbook table

ajSeqPrinthtmlInFormat Reports the internal data structures as an HTML table

ajSeqPrintwikiInFormat Reports the internal data structures as a wiki table

ajSeqFormatTest tests whether a named format is known

ajSeqUsaGetBase Extracts the base part from a USA, suitable for use in fetching other sequences from the same source

Function ajSeqsetRead

Parse a USA Uniform Sequence Address into format, access, file and entry

Prototype

AjBool ajSeqsetRead (
      AjPSeqset thys,
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeqset thys Output Sequence set returned.

AjPSeqin seqin Modify Sequence input definitions

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPSeqset`	`thys`	Output	Sequence set returned.
`AjPSeqin`	`seqin`	Modify	Sequence input definitions
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 1.0.0

Function ajSeqsetallRead

Parse a USA Uniform Sequence Address into format, access, file and entry

Prototype

AjBool ajSeqsetallRead (
      AjPList thys,
      AjPSeqin seqin
);

Type Name Read/Write Description

AjPList thys Output List of sequence sets returned.

AjPSeqin seqin Modify Sequence input definitions

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPList`	`thys`	Output	List of sequence sets returned.
`AjPSeqin`	`seqin`	Modify	Sequence input definitions
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 2.8.0

Function ajSeqsetFromList

Builds a sequence set from a list of sequences

Prototype

ajint ajSeqsetFromList (
      AjPSeqset thys,
      const AjPList list
);

Type Name Read/Write Description

AjPSeqset thys Output Sequence set

const AjPList list Input List of sequence objects

ajint RETURN Number of sequences in the set.

Type	Name	Read/Write	Description
`AjPSeqset`	`thys`	Output	Sequence set
`const AjPList`	`list`	Input	List of sequence objects
`ajint`		RETURN	Number of sequences in the set.

From EMBOSS 2.1.0

Function ajSeqsetFromPair

Builds a sequence set from a pair of sequences

Prototype

ajint ajSeqsetFromPair (
      AjPSeqset thys,
      const AjPSeq seqa,
      const AjPSeq seqb
);

Type Name Read/Write Description

AjPSeqset thys Output Sequence set

const AjPSeq seqa Input Sequence 1

const AjPSeq seqb Input Sequence 2

ajint RETURN Number of sequences in the set.

Type	Name	Read/Write	Description
`AjPSeqset`	`thys`	Output	Sequence set
`const AjPSeq`	`seqa`	Input	Sequence 1
`const AjPSeq`	`seqb`	Input	Sequence 2
`ajint`		RETURN	Number of sequences in the set.

From EMBOSS 2.1.0

Function ajSeqsetApp

Adds a sequence to a sequence set

Prototype

ajint ajSeqsetApp (
      AjPSeqset thys,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPSeqset thys Output Sequence set

const AjPSeq seq Input Sequence

ajint RETURN Number of sequences in the set.

Type	Name	Read/Write	Description
`AjPSeqset`	`thys`	Output	Sequence set
`const AjPSeq`	`seq`	Input	Sequence
`ajint`		RETURN	Number of sequences in the set.

From EMBOSS 2.1.0

Function ajSeqPrintInFormat

Reports the internal data structures

Prototype

void ajSeqPrintInFormat (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full report (usually ajFalse)

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`AjBool`	`full`	Input	Full report (usually ajFalse)
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqPrintbookInFormat

Reports the internal data structures as a Docbook table

Prototype

void ajSeqPrintbookInFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.2.0

Function ajSeqPrinthtmlInFormat

Reports the internal data structures as an HTML table

Prototype

void ajSeqPrinthtmlInFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.2.0

Function ajSeqPrintwikiInFormat

Reports the internal data structures as a wiki table

Prototype

void ajSeqPrintwikiInFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.2.0

Function ajSeqFormatTest

tests whether a named format is known

Prototype

AjBool ajSeqFormatTest (
      const AjPStr format
);

Type Name Read/Write Description

const AjPStr format Input Format

AjBool RETURN ajTrue if formats was accepted

Type	Name	Read/Write	Description
`const AjPStr`	`format`	Input	Format
`AjBool`		RETURN	ajTrue if formats was accepted

From EMBOSS 2.7.0

Function ajSeqUsaGetBase

Extracts the base part from a USA, suitable for use in fetching other sequences from the same source

Prototype

AjBool ajSeqUsaGetBase (
      const AjPStr usa,
      AjPStr* Pbaseusa
);

Type Name Read/Write Description

const AjPStr usa Input Original USA

AjPStr* Pbaseusa Modify Base part of USA

AjBool RETURN True on success

Type	Name	Read/Write	Description
`const AjPStr`	`usa`	Input	Original USA
`AjPStr*`	`Pbaseusa`	Modify	Base part of USA
`AjBool`		RETURN	True on success

From EMBOSS 6.1.0

Section: Sequence Query Operators

These functions use the contents of a sequence query object but do not make any changes.

Functions:

ajSeqParseFasta Parse an NCBI format fasta line. Return id acc sv and description

ajSeqParseNcbi Parse an NCBI format fasta line. Return id acc and description.

ajSeqParseFastq Parse a fastq id line. Return id acc sv and description

ajSeqGetFromUsaRange Returns a sequence given a USA

ajSeqGetFromUsa Returns a sequence given a USA

ajSeqsetGetFromUsa Return a seqset given a usa

ajSeqReadExit Cleans up sequence reading internal memory

Function ajSeqParseFasta

Parse an NCBI format fasta line. Return id acc sv and description

Prototype

AjBool ajSeqParseFasta (
      const AjPStr instr,
      AjPStr* id,
      AjPStr* acc,
      AjPStr* sv,
      AjPStr* desc
);

Type Name Read/Write Description

const AjPStr instr Input fasta line.

AjPStr* id Output id.

AjPStr* acc Output accession number.

AjPStr* sv Output sequence version number.

AjPStr* desc Output description.

AjBool RETURN ajTrue if fasta format

Type	Name	Read/Write	Description
`const AjPStr`	`instr`	Input	fasta line.
`AjPStr*`	`id`	Output	id.
`AjPStr*`	`acc`	Output	accession number.
`AjPStr*`	`sv`	Output	sequence version number.
`AjPStr*`	`desc`	Output	description.
`AjBool`		RETURN	ajTrue if fasta format

From EMBOSS 2.0.0

Function ajSeqParseNcbi

Parse an NCBI format fasta line. Return id acc and description.

Prototype

AjBool ajSeqParseNcbi (
      const AjPStr instr,
      AjPStr* id,
      AjPStr* acc,
      AjPStr* sv,
      AjPStr* gi,
      AjPStr* db,
      AjPStr* desc
);

Type Name Read/Write Description

const AjPStr instr Input fasta line.

AjPStr* id Output id.

AjPStr* acc Output accession number.

AjPStr* sv Output sequence version number.

AjPStr* gi Output GI version number.

AjPStr* db Output NCBI database name

AjPStr* desc Output description.

AjBool RETURN ajTrue if ncbi format

Type	Name	Read/Write	Description
`const AjPStr`	`instr`	Input	fasta line.
`AjPStr*`	`id`	Output	id.
`AjPStr*`	`acc`	Output	accession number.
`AjPStr*`	`sv`	Output	sequence version number.
`AjPStr*`	`gi`	Output	GI version number.
`AjPStr*`	`db`	Output	NCBI database name
`AjPStr*`	`desc`	Output	description.
`AjBool`		RETURN	ajTrue if ncbi format

From EMBOSS 1.0.0

Function ajSeqParseFastq

Parse a fastq id line. Return id acc sv and description

Prototype

AjBool ajSeqParseFastq (
      const AjPStr instr,
      AjPStr* id,
      AjPStr* desc
);

Type Name Read/Write Description

const AjPStr instr Input fastq line.

AjPStr* id Output id.

AjPStr* desc Output description.

AjBool RETURN ajTrue if fastq format

Type	Name	Read/Write	Description
`const AjPStr`	`instr`	Input	fastq line.
`AjPStr*`	`id`	Output	id.
`AjPStr*`	`desc`	Output	description.
`AjBool`		RETURN	ajTrue if fastq format

From EMBOSS 6.1.0

Function ajSeqGetFromUsaRange

Returns a sequence given a USA

Prototype

AjBool ajSeqGetFromUsaRange (
      const AjPStr thys,
      AjBool protein,
      ajint ibegin,
      ajint iend,
      AjPSeq seq
);

Type Name Read/Write Description

const AjPStr thys Input USA

AjBool protein Input True if protein

ajint ibegin Input sequence start position

ajint iend Input sequence end position

AjPSeq seq Modify sequence

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	USA
`AjBool`	`protein`	Input	True if protein
`ajint`	`ibegin`	Input	sequence start position
`ajint`	`iend`	Input	sequence end position
`AjPSeq`	`seq`	Modify	sequence
`AjBool`		RETURN	ajTrue on success

From EMBOSS 6.4.0

Function ajSeqGetFromUsa

Returns a sequence given a USA

Prototype

AjBool ajSeqGetFromUsa (
      const AjPStr thys,
      AjBool protein,
      AjPSeq seq
);

Type Name Read/Write Description

const AjPStr thys Input USA

AjBool protein Input True if protein

AjPSeq seq Modify sequence

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	USA
`AjBool`	`protein`	Input	True if protein
`AjPSeq`	`seq`	Modify	sequence
`AjBool`		RETURN	ajTrue on success

From EMBOSS 1.8.0

Function ajSeqsetGetFromUsa

Return a seqset given a usa

Prototype

AjBool ajSeqsetGetFromUsa (
      const AjPStr thys,
      AjPSeqset* seq
);

Type Name Read/Write Description

const AjPStr thys Input usa

AjPSeqset* seq Output seqset

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	usa
`AjPSeqset*`	`seq`	Output	seqset
`AjBool`		RETURN	ajTrue on success

From EMBOSS 2.7.0

Function ajSeqReadExit

Cleans up sequence reading internal memory

Prototype

void ajSeqReadExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0

Section: Internals

Functions to return internal values

Functions:

ajSeqinTypeGetFields Returns the listof known field names for ajSeqinRead

ajSeqinTypeGetQlinks Returns the listof known query link operators for ajSeqRead

ajSeqinTrace Debug calls to trace the data in a sequence input object.

ajSeqaccessGetDb returns the table in which sequence database access details are registered

ajSeqaccessMethodGetQlinks Tests for a named method for sequence reading and returns the known query link operators

ajSeqaccessMethodGetScope Tests for a named method for sequence reading and returns the scope (entry, query or all).

ajSeqaccessMethodTest Tests for a named method for sequence reading.

ajSeqinformatTerm Tests whether a data input format termis known

ajSeqinformatTest Tests whether a named sequence data input format is known

Function ajSeqinTypeGetFields

Returns the listof known field names for ajSeqinRead

Prototype

const char* ajSeqinTypeGetFields (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

Type	Name	Read/Write	Description
`const char*`		RETURN	List of field names

From EMBOSS 6.4.0

Function ajSeqinTypeGetQlinks

Returns the listof known query link operators for ajSeqRead

Prototype

const char* ajSeqinTypeGetQlinks (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

Type	Name	Read/Write	Description
`const char*`		RETURN	List of field names

From EMBOSS 6.4.0

Function ajSeqinTrace

Debug calls to trace the data in a sequence input object.

Prototype

void ajSeqinTrace (
      const AjPSeqin thys
);

Type Name Read/Write Description

const AjPSeqin thys Input Sequence input object.

void RETURN

Type	Name	Read/Write	Description
`const AjPSeqin`	`thys`	Input	Sequence input object.
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqaccessGetDb

returns the table in which sequence database access details are registered

Prototype

AjPTable ajSeqaccessGetDb (
      void
);

Type Name Read/Write Description

AjPTable RETURN Access functions hash table

Type	Name	Read/Write	Description
`AjPTable`		RETURN	Access functions hash table

From EMBOSS 6.4.0

Function ajSeqaccessMethodGetQlinks

Tests for a named method for sequence reading and returns the known query link operators

Prototype

const char* ajSeqaccessMethodGetQlinks (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

const char* RETURN Known link operators

Type	Name	Read/Write	Description
`const AjPStr`	`method`	Input	Method required.
`const char*`		RETURN	Known link operators

From EMBOSS 6.4.0

Function ajSeqaccessMethodGetScope

Tests for a named method for sequence reading and returns the scope (entry, query or all).

Prototype

ajuint ajSeqaccessMethodGetScope (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

ajuint RETURN Scope flags

Type	Name	Read/Write	Description
`const AjPStr`	`method`	Input	Method required.
`ajuint`		RETURN	Scope flags

From EMBOSS 6.4.0

Function ajSeqaccessMethodTest

Tests for a named method for sequence reading.

Prototype

AjBool ajSeqaccessMethodTest (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`const AjPStr`	`method`	Input	Method required.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.4.0

Function ajSeqinformatTerm

Tests whether a data input format termis known

Prototype

AjBool ajSeqinformatTerm (
      const AjPStr term
);

Type Name Read/Write Description

const AjPStr term Input Format term EDAM ID

AjBool RETURN ajTrue if term was accepted

Type	Name	Read/Write	Description
`const AjPStr`	`term`	Input	Format term EDAM ID
`AjBool`		RETURN	ajTrue if term was accepted

From EMBOSS 6.4.0

Function ajSeqinformatTest

Tests whether a named sequence data input format is known

Prototype

AjBool ajSeqinformatTest (
      const AjPStr format
);

Type Name Read/Write Description

const AjPStr format Input Format

AjBool RETURN ajTrue if formats was accepted

Type	Name	Read/Write	Description
`const AjPStr`	`format`	Input	Format
`AjBool`		RETURN	ajTrue if formats was accepted

From EMBOSS 6.4.0

ajSeqinUsa	Creates or resets a sequence input object using a new Universal Sequence Address
ajSeqinSetNuc	Sets the type to be forced as nucleic for a sequence input object
ajSeqinSetProt	Sets the type to be forced as protein for a sequence input object
ajSeqinSetRange	Sets the start and end positions for a sequence input object

ajSeqAllRead	Parse a USA Uniform Sequence Address into format, access, file and entry
ajSeqallFile	Parse a USA Uniform Sequence Address
ajSeqallNext	Reads the next sequence into a sequence stream. For the first call this simply returns the sequence already loaded. For later calls a new sequence is read.
ajSeqinClearPos	Clears a Sequence input object position information as possibly read from a USA that included the begin, end and direction
ajSeqinClear	Clears a Sequence input object back to "as new" condition, except for the USA list and the features setting which must be preserved.

ajSeqsetRead	Parse a USA Uniform Sequence Address into format, access, file and entry
ajSeqsetallRead	Parse a USA Uniform Sequence Address into format, access, file and entry
ajSeqsetFromList	Builds a sequence set from a list of sequences
ajSeqsetFromPair	Builds a sequence set from a pair of sequences
ajSeqsetApp	Adds a sequence to a sequence set
ajSeqPrintInFormat	Reports the internal data structures
ajSeqPrintbookInFormat	Reports the internal data structures as a Docbook table
ajSeqPrinthtmlInFormat	Reports the internal data structures as an HTML table
ajSeqPrintwikiInFormat	Reports the internal data structures as a wiki table
ajSeqFormatTest	tests whether a named format is known
ajSeqUsaGetBase	Extracts the base part from a USA, suitable for use in fetching other sequences from the same source

ajSeqParseFasta	Parse an NCBI format fasta line. Return id acc sv and description
ajSeqParseNcbi	Parse an NCBI format fasta line. Return id acc and description.
ajSeqParseFastq	Parse a fastq id line. Return id acc sv and description
ajSeqGetFromUsaRange	Returns a sequence given a USA
ajSeqGetFromUsa	Returns a sequence given a USA
ajSeqsetGetFromUsa	Return a seqset given a usa
ajSeqReadExit	Cleans up sequence reading internal memory

ajSeqinTypeGetFields	Returns the listof known field names for ajSeqinRead
ajSeqinTypeGetQlinks	Returns the listof known query link operators for ajSeqRead
ajSeqinTrace	Debug calls to trace the data in a sequence input object.
ajSeqaccessGetDb	returns the table in which sequence database access details are registered
ajSeqaccessMethodGetQlinks	Tests for a named method for sequence reading and returns the known query link operators
ajSeqaccessMethodGetScope	Tests for a named method for sequence reading and returns the scope (entry, query or all).
ajSeqaccessMethodTest	Tests for a named method for sequence reading.
ajSeqinformatTerm	Tests whether a data input format termis known
ajSeqinformatTest	Tests whether a named sequence data input format is known