ajassemread.c

Datatypes:

AjPAssemin Assembly input objects

none Miscellaneous

AjPTable Internal call register table

none Input formats

Datatype: AjPAssemin

Function is for manipulating assembly input objects

Sections:

Assembly Input Constructors Constructors

Assembly Input Destructors Destructors

assembly input modifiers Modifiers

casts Casts

Assembly data inputs Input

AjPAssemin: Assembly Input Constructors

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

Functions:

ajAsseminNew Creates a new assembly input object.

Function ajAsseminNew

Creates a new assembly input object.

Prototype

AjPAssemin ajAsseminNew (
      void
);

Type Name Read/Write Description

AjPAssemin RETURN New assembly input object.

Type	Name	Read/Write	Description
`AjPAssemin`		RETURN	New assembly input object.

From EMBOSS 6.4.0

AjPAssemin: Assembly Input Destructors

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

Functions:

ajAsseminDel Deletes an assembly input object.

Function ajAsseminDel

Deletes an assembly input object.

Prototype

void ajAsseminDel (
      AjPAssemin* pthis
);

Type Name Read/Write Description

AjPAssemin* pthis Delete Assembly input

void RETURN

Type	Name	Read/Write	Description
`AjPAssemin*`	`pthis`	Delete	Assembly input
`void`		RETURN

From EMBOSS 6.4.0

AjPAssemin: assembly input modifiers

These functions use the contents of an assembly input object and update them.

Functions:

ajAsseminClear Clears an assembly input object back to "as new" condition, except for the query list which must be preserved.

ajAsseminQryC Resets an assembly input object using a new Universal Query Address

ajAsseminQryS Resets an assembly input object using a new Universal Query Address

Function ajAsseminClear

Clears an assembly input object back to "as new" condition, except for the query list which must be preserved.

Prototype

void ajAsseminClear (
      AjPAssemin thys
);

Type Name Read/Write Description

AjPAssemin thys Output Assembly input

void RETURN

Type	Name	Read/Write	Description
`AjPAssemin`	`thys`	Output	Assembly input
`void`		RETURN

From EMBOSS 6.4.0

Function ajAsseminQryC

Resets an assembly input object using a new Universal Query Address

Prototype

void ajAsseminQryC (
      AjPAssemin thys,
      const char* txt
);

Type Name Read/Write Description

AjPAssemin thys Modify Assembly input object.

const char* txt Input Query

void RETURN

Type	Name	Read/Write	Description
`AjPAssemin`	`thys`	Modify	Assembly input object.
`const char*`	`txt`	Input	Query
`void`		RETURN

From EMBOSS 6.4.0

Function ajAsseminQryS

Resets an assembly input object using a new Universal Query Address

Prototype

void ajAsseminQryS (
      AjPAssemin thys,
      const AjPStr str
);

Type Name Read/Write Description

AjPAssemin thys Modify Assembly input object.

const AjPStr str Input Query

void RETURN

Type	Name	Read/Write	Description
`AjPAssemin`	`thys`	Modify	Assembly input object.
`const AjPStr`	`str`	Input	Query
`void`		RETURN

From EMBOSS 6.4.0

AjPAssemin: casts

Return values

Functions:

ajAsseminTrace Debug calls to trace the data in an assembly input object.

Function ajAsseminTrace

Debug calls to trace the data in an assembly input object.

Prototype

void ajAsseminTrace (
      const AjPAssemin thys
);

Type Name Read/Write Description

const AjPAssemin thys Input Assembly input object.

void RETURN

Type	Name	Read/Write	Description
`const AjPAssemin`	`thys`	Input	Assembly input object.
`void`		RETURN

From EMBOSS 6.4.0

AjPAssemin: Assembly data inputs

These functions read the assembly data provided by the first argument

Functions:

ajAsseminRead If the file is not yet open, calls asseminQryProcess to convert the query into an open file stream.

Function ajAsseminRead

If the file is not yet open, calls asseminQryProcess to convert the query into an open file stream.

Prototype

AjBool ajAsseminRead (
      AjPAssemin assemin,
      AjPAssem assem
);

Type Name Read/Write Description

AjPAssemin assemin Modify assembly data input definitions

AjPAssem assem Output assembly data returned.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPAssemin`	`assemin`	Modify	assembly data input definitions
`AjPAssem`	`assem`	Output	assembly data returned.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.4.0

Datatype: none

Assembly input internals

Sections:

Print Casts

Miscellaneous Miscellaneous

Internals Miscellaneous

Section: Print

Printing to a file

Functions:

ajAsseminprintBook Reports the internal data structures as a Docbook table

ajAsseminprintHtml Reports the internal data structures as an HTML table

ajAsseminprintText Reports the internal data structures

ajAsseminprintWiki Reports the internal data structures as a wiki table

Function ajAsseminprintBook

Reports the internal data structures as a Docbook table

Prototype

void ajAsseminprintBook (
      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 6.4.0

Function ajAsseminprintHtml

Reports the internal data structures as an HTML table

Prototype

void ajAsseminprintHtml (
      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 6.4.0

Function ajAsseminprintText

Reports the internal data structures

Prototype

void ajAsseminprintText (
      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 6.4.0

Function ajAsseminprintWiki

Reports the internal data structures as a wiki table

Prototype

void ajAsseminprintWiki (
      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 6.4.0

Section: Miscellaneous

Functions to initialise and clean up internals

Functions:

ajAsseminExit Cleans up assembly input internal memory

Function ajAsseminExit

Cleans up assembly input internal memory

Prototype

void ajAsseminExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.4.0

Section: Internals

Functions to return internal values

Functions:

ajAsseminTypeGetFields Returns the listof known field names for ajAsseminRead

ajAsseminTypeGetQlinks Returns the listof known query link operators for ajAsseminRead

Function ajAsseminTypeGetFields

Returns the listof known field names for ajAsseminRead

Prototype

const char* ajAsseminTypeGetFields (
      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 ajAsseminTypeGetQlinks

Returns the listof known query link operators for ajAsseminRead

Prototype

const char* ajAsseminTypeGetQlinks (
      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

Datatype: AjPTable

Functions to manage the internal call register table that links the ajaxdb library functions with code in the core AJAX library.

Sections:

Cast Casts

AjPTable: Cast

Return a reference to the call table

Functions:

ajAssemaccessGetDb Returns the table in which assembly database access details are registered

ajAssemaccessMethodGetQlinks Tests for a named method for assembly data reading returns the known query link operators

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

ajAssemaccessMethodTest Tests for a named method for assembly data reading.

Function ajAssemaccessGetDb

Returns the table in which assembly database access details are registered

Prototype

AjPTable ajAssemaccessGetDb (
      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 ajAssemaccessMethodGetQlinks

Tests for a named method for assembly data reading returns the known query link operators

Prototype

const char* ajAssemaccessMethodGetQlinks (
      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 ajAssemaccessMethodGetScope

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

Prototype

ajuint ajAssemaccessMethodGetScope (
      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 ajAssemaccessMethodTest

Tests for a named method for assembly data reading.

Prototype

AjBool ajAssemaccessMethodTest (
      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

Datatype: none

Input formats internals

Sections:

cast Casts

Section: cast

Values for input formats

Functions:

ajAsseminformatTerm Tests whether a assembly data input format term is known

ajAsseminformatTest Tests whether a named assembly data input format is known

Function ajAsseminformatTerm

Tests whether a assembly data input format term is known

Prototype

AjBool ajAsseminformatTerm (
      const AjPStr term
);

Type Name Read/Write Description

const AjPStr term Input Format term EDAM ID

AjBool RETURN ajTrue if formats was accepted

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

From EMBOSS 6.4.0

Function ajAsseminformatTest

Tests whether a named assembly data input format is known

Prototype

AjBool ajAsseminformatTest (
      const AjPStr format
);

Type Name Read/Write Description

const AjPStr format Input Format

AjBool RETURN ajTrue if format was accepted

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

From EMBOSS 6.4.0

AjPAssemin	Assembly input objects
none	Miscellaneous
AjPTable	Internal call register table
none	Input formats

Assembly Input Constructors	Constructors
Assembly Input Destructors	Destructors
assembly input modifiers	Modifiers
casts	Casts
Assembly data inputs	Input

ajAsseminClear	Clears an assembly input object back to "as new" condition, except for the query list which must be preserved.
ajAsseminQryC	Resets an assembly input object using a new Universal Query Address
ajAsseminQryS	Resets an assembly input object using a new Universal Query Address

ajAsseminprintBook	Reports the internal data structures as a Docbook table
ajAsseminprintHtml	Reports the internal data structures as an HTML table
ajAsseminprintText	Reports the internal data structures
ajAsseminprintWiki	Reports the internal data structures as a wiki table

ajAsseminTypeGetFields	Returns the listof known field names for ajAsseminRead
ajAsseminTypeGetQlinks	Returns the listof known query link operators for ajAsseminRead

ajAssemaccessGetDb	Returns the table in which assembly database access details are registered
ajAssemaccessMethodGetQlinks	Tests for a named method for assembly data reading returns the known query link operators
ajAssemaccessMethodGetScope	Tests for a named method for assembly data reading and returns the scope (entry, query or all).
ajAssemaccessMethodTest	Tests for a named method for assembly data reading.

ajAsseminformatTerm	Tests whether a assembly data input format term is known
ajAsseminformatTest	Tests whether a named assembly data input format is known