ajassemread.c

Datatypes:
AjPAssemin Assembly input objects
none Miscellaneous
AjPTable Internal call register table
AjPAssemload Assembly Loader
none Input formats

Datatype: AjPAssemin

Function is for manipulating assembly input objects

Sections:
Assembly Input ConstructorsConstructors
Assembly Input DestructorsDestructors
assembly input modifiersModifiers
castsCasts
Assembly data inputsInput

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:
ajAsseminNewCreates a new assembly input object.

Function ajAsseminNew

Creates a new assembly input object.

Prototype

AjPAssemin ajAsseminNew (
      void
);

TypeNameRead/WriteDescription
AjPAssemin RETURNNew 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:
ajAsseminDelDeletes an assembly input object.

Function ajAsseminDel

Deletes an assembly input object.

Prototype

void ajAsseminDel (
      AjPAssemin* pthis
);

TypeNameRead/WriteDescription
AjPAssemin*pthisDeleteAssembly 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:
ajAsseminClearClears an assembly input object back to "as new" condition, except for the query list which must be preserved.
ajAsseminQryCResets an assembly input object using a new Universal Query Address
ajAsseminQrySResets 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
);

TypeNameRead/WriteDescription
AjPAsseminthysOutputAssembly 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
);

TypeNameRead/WriteDescription
AjPAsseminthysModifyAssembly input object.
const char*txtInputQuery
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
);

TypeNameRead/WriteDescription
AjPAsseminthysModifyAssembly input object.
const AjPStrstrInputQuery
void RETURN

From EMBOSS 6.4.0

AjPAssemin: casts

Return values

Functions:
ajAsseminTraceDebug 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
);

TypeNameRead/WriteDescription
const AjPAsseminthysInputAssembly input object.
void RETURN

From EMBOSS 6.4.0

AjPAssemin: Assembly data inputs

These functions load the assembly data provided by the first argument

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

Function ajAsseminLoad

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

Prototype

AjBool ajAsseminLoad (
      AjPAssemin assemin,
      AjPAssem assem
);

TypeNameRead/WriteDescription
AjPAsseminasseminModifyassembly data input definitions
AjPAssemassemOutputassembly data returned.
AjBool RETURNajTrue on success.

From EMBOSS 6.5.0

Datatype: none

Assembly input internals

Sections:
PrintCasts
MiscellaneousMiscellaneous
InternalsMiscellaneous

Section: Print

Printing to a file

Functions:
ajAsseminprintBookReports the internal data structures as a Docbook table
ajAsseminprintHtmlReports the internal data structures as an HTML table
ajAsseminprintTextReports the internal data structures
ajAsseminprintWikiReports the internal data structures as a wiki table

Function ajAsseminprintBook

Reports the internal data structures as a Docbook table

Prototype

void ajAsseminprintBook (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Function ajAsseminprintHtml

Reports the internal data structures as an HTML table

Prototype

void ajAsseminprintHtml (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Function ajAsseminprintText

Reports the internal data structures

Prototype

void ajAsseminprintText (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull 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
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Section: Miscellaneous

Functions to initialise and clean up internals

Functions:
ajAsseminExitCleans up assembly input internal memory

Function ajAsseminExit

Cleans up assembly input internal memory

Prototype

void ajAsseminExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 6.4.0

Section: Internals

Functions to return internal values

Functions:
ajAsseminTypeGetFieldsReturns the listof known field names for ajAsseminLoad
ajAsseminTypeGetQlinksReturns the listof known query link operators for ajAsseminLoad

Function ajAsseminTypeGetFields

Returns the listof known field names for ajAsseminLoad

Prototype

const char* ajAsseminTypeGetFields (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList of field names

From EMBOSS 6.4.0

Function ajAsseminTypeGetQlinks

Returns the listof known query link operators for ajAsseminLoad

Prototype

const char* ajAsseminTypeGetQlinks (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList 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:
CastCasts

AjPTable: Cast

Return a reference to the call table

Functions:
ajAssemaccessGetDbReturns the table in which assembly database access details are registered
ajAssemaccessMethodGetQlinksTests for a named method for assembly data reading returns the known query link operators
ajAssemaccessMethodGetScopeTests for a named method for assembly data reading and returns the scope (entry, query or all).
ajAssemaccessMethodTestTests 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
);

TypeNameRead/WriteDescription
AjPTable RETURNAccess 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
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
const char* RETURNKnown 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
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
ajuint RETURNScope flags

From EMBOSS 6.4.0

Function ajAssemaccessMethodTest

Tests for a named method for assembly data reading.

Prototype

AjBool ajAssemaccessMethodTest (
      const AjPStr method
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
AjBool RETURNajTrue on success.

From EMBOSS 6.4.0

Datatype: AjPAssemload

Function is for manipulating assembly loader objects

Sections:
Assembly Loader ConstructorsConstructors
Assembly Loader DestructorsDestructors
Assembly loader modifiersModifiers
Assembly loadingInput

AjPAssemload: Assembly Loader Constructors

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

Functions:
ajAssemloadNewCreates a new assembly loader object.

Function ajAssemloadNew

Creates a new assembly loader object.

Prototype

AjPAssemload ajAssemloadNew (
      void
);

TypeNameRead/WriteDescription
AjPAssemload RETURNNew assembly loader object.

From EMBOSS 6.5.0

AjPAssemload: Assembly Loader Destructors

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

Functions:
ajAssemloadDelDeletes an assembly loader object.

Function ajAssemloadDel

Deletes an assembly loader object.

Prototype

void ajAssemloadDel (
      AjPAssemload* pthis
);

TypeNameRead/WriteDescription
AjPAssemload*pthisDeleteAssembly loader
void RETURN

From EMBOSS 6.5.0

AjPAssemload: Assembly loader modifiers

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

Functions:
ajAssemloadClearClears an assembly loader object back to "as new" condition, except for the query list which must be preserved.

Function ajAssemloadClear

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

Prototype

void ajAssemloadClear (
      AjPAssemload thys
);

TypeNameRead/WriteDescription
AjPAssemloadthysOutputAssembly loader
void RETURN

From EMBOSS 6.5.0

AjPAssemload: Assembly loading

These functions use an assembly loader object to read data

Functions:
ajAssemloadMoreTest whether more assembly data can be loaded
ajAssemloadNextParse an assembly query into format, access, file and entry

Function ajAssemloadMore

Test whether more assembly data can be loaded

Prototype

AjBool ajAssemloadMore (
      AjPAssemload thys,
      AjPAssem* Passem
);

TypeNameRead/WriteDescription
AjPAssemloadthysOutputAssembly loader
AjPAssem*PassemModifyAssembly updated
AjBool RETURNajTrue on success.

From EMBOSS 6.5.0

Function ajAssemloadNext

Parse an assembly query into format, access, file and entry

Prototype

AjBool ajAssemloadNext (
      AjPAssemload thys,
      AjPAssem* Passem
);

TypeNameRead/WriteDescription
AjPAssemloadthysOutputAssembly loader
AjPAssem*PassemModifyAssembly returned
AjBool RETURNajTrue on success.

From EMBOSS 6.5.0

Datatype: none

Input formats internals

Sections:
castCasts

Section: cast

Values for input formats

Functions:
ajAsseminformatTermTests whether a assembly data input format term is known
ajAsseminformatTestTests 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
);

TypeNameRead/WriteDescription
const AjPStrtermInputFormat term EDAM ID
AjBool RETURNajTrue 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
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat
AjBool RETURNajTrue if format was accepted

From EMBOSS 6.4.0