ajvarread.c

Datatypes:
AjPVarin Variation input objects
none Miscellaneous
AjPTable Internal call register table
AjPVarall Variation Input Stream
none Input formats

Datatype: AjPVarin

Function is for manipulating variation input objects

Sections:
Variation input constructorsConstructors
variation input destructorsDestructors
variation input modifiersModifiers
castsCasts
Variation data inputsInput

AjPVarin: Variation input constructors

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

Functions:
ajVarinNewCreates a new variation input object.

Function ajVarinNew

Creates a new variation input object.

Prototype

AjPVarin ajVarinNew (
      void
);

TypeNameRead/WriteDescription
AjPVarin RETURNNew variation input object.

From EMBOSS 6.4.0

AjPVarin: variation input destructors

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

Functions:
ajVarinDelDeletes a variation input object.

Function ajVarinDel

Deletes a variation input object.

Prototype

void ajVarinDel (
      AjPVarin* pthis
);

TypeNameRead/WriteDescription
AjPVarin*pthisDeleteVariation input
void RETURN

From EMBOSS 6.4.0

AjPVarin: variation input modifiers

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

Functions:
ajVarinClearClears a variation input object back to "as new" condition, except for the query list which must be preserved.
ajVarinQryCResets a variation input object using a new Universal Query Address
ajVarinQrySResets a variation input object using a new Universal Query Address

Function ajVarinClear

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

Prototype

void ajVarinClear (
      AjPVarin thys
);

TypeNameRead/WriteDescription
AjPVarinthysOutputVariation input
void RETURN

From EMBOSS 6.4.0

Function ajVarinQryC

Resets a variation input object using a new Universal Query Address

Prototype

void ajVarinQryC (
      AjPVarin thys,
      const char* txt
);

TypeNameRead/WriteDescription
AjPVarinthysModifyVariation input object.
const char*txtInputQuery
void RETURN

From EMBOSS 6.4.0

Function ajVarinQryS

Resets a variation input object using a new Universal Query Address

Prototype

void ajVarinQryS (
      AjPVarin thys,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPVarinthysModifyVariation input object.
const AjPStrstrInputQuery
void RETURN

From EMBOSS 6.4.0

AjPVarin: casts

Return values

Functions:
ajVarinTraceDebug calls to trace the data in a variation input object.

Function ajVarinTrace

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

Prototype

void ajVarinTrace (
      const AjPVarin thys
);

TypeNameRead/WriteDescription
const AjPVarinthysInputVariation input object.
void RETURN

From EMBOSS 6.4.0

AjPVarin: Variation data inputs

These functions read the wxyxdesc data provided by the first argument

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

Function ajVarinRead

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

Prototype

AjBool ajVarinRead (
      AjPVarin varin,
      AjPVar var
);

TypeNameRead/WriteDescription
AjPVarinvarinModifyVariation data input definitions
AjPVarvarOutputVariation data returned.
AjBool RETURNajTrue on success.

From EMBOSS 6.4.0

Datatype: none

Variation input internals

Sections:
PrintCasts
MiscellaneousMiscellaneous
InternalsMiscellaneous

Section: Print

Printing to a file

Functions:
ajVarinprintBookReports the internal data structures as a Docbook table
ajVarinprintHtmlReports the internal data structures as an HTML table
ajVarinprintTextReports the internal data structures
ajVarinprintWikiReports the internal data structures as a wiki table

Function ajVarinprintBook

Reports the internal data structures as a Docbook table

Prototype

void ajVarinprintBook (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Function ajVarinprintHtml

Reports the internal data structures as an HTML table

Prototype

void ajVarinprintHtml (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Function ajVarinprintText

Reports the internal data structures

Prototype

void ajVarinprintText (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull report (usually ajFalse)
void RETURN

From EMBOSS 6.4.0

Function ajVarinprintWiki

Reports the internal data structures as a wiki table

Prototype

void ajVarinprintWiki (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Section: Miscellaneous

Functions to initialise and clean up internals

Functions:
ajVarinExitCleans up variation input internal memory

Function ajVarinExit

Cleans up variation input internal memory

Prototype

void ajVarinExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 6.4.0

Section: Internals

Functions to return internal values

Functions:
ajVarinTypeGetFieldsReturns the list of known field names for ajVarinRead
ajVarinTypeGetQlinksReturns the listof known query link operators for ajVarinRead

Function ajVarinTypeGetFields

Returns the list of known field names for ajVarinRead

Prototype

const char* ajVarinTypeGetFields (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList of field names

From EMBOSS 6.4.0

Function ajVarinTypeGetQlinks

Returns the listof known query link operators for ajVarinRead

Prototype

const char* ajVarinTypeGetQlinks (
      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:
ajVaraccessGetDbReturns the table in which variation database access details are registered
ajVaraccessMethodGetQlinksTests for a named method for var data reading returns the known query link operators
ajVaraccessMethodGetScopeTests for a named method for variation data reading and returns the scope (entry, query or all).
ajVaraccessMethodTestTests for a named method for variation data reading.

Function ajVaraccessGetDb

Returns the table in which variation database access details are registered

Prototype

AjPTable ajVaraccessGetDb (
      void
);

TypeNameRead/WriteDescription
AjPTable RETURNAccess functions hash table

From EMBOSS 6.4.0

Function ajVaraccessMethodGetQlinks

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

Prototype

const char* ajVaraccessMethodGetQlinks (
      const AjPStr method
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
const char* RETURNKnown link operators

From EMBOSS 6.4.0

Function ajVaraccessMethodGetScope

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

Prototype

ajuint ajVaraccessMethodGetScope (
      const AjPStr method
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
ajuint RETURNScope flags

From EMBOSS 6.4.0

Function ajVaraccessMethodTest

Tests for a named method for variation data reading.

Prototype

AjBool ajVaraccessMethodTest (
      const AjPStr method
);

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

From EMBOSS 6.4.0

Datatype: AjPVarall

Function is for manipulating variation input stream objects

Sections:
Variation Input ConstructorsConstructors
Variation Input Stream DestructorsDestructors
Variation input stream modifiersModifiers
Variation input stream castsCasts
Variation inputGeneral use

AjPVarall: Variation Input Constructors

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

Functions:
ajVarallNewCreates a new variation input stream object.

Function ajVarallNew

Creates a new variation input stream object.

Prototype

AjPVarall ajVarallNew (
      void
);

TypeNameRead/WriteDescription
AjPVarall RETURNNew variation input stream object.

From EMBOSS 6.4.0

AjPVarall: Variation Input Stream Destructors

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

Functions:
ajVarallDelDeletes a variation input stream object.

Function ajVarallDel

Deletes a variation input stream object.

Prototype

void ajVarallDel (
      AjPVarall* pthis
);

TypeNameRead/WriteDescription
AjPVarall*pthisDeleteVariation input stream
void RETURN

From EMBOSS 6.4.0

AjPVarall: Variation input stream modifiers

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

Functions:
ajVarallClearClears a variation input stream object back to "as new" condition, except for the query list which must be preserved.

Function ajVarallClear

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

Prototype

void ajVarallClear (
      AjPVarall thys
);

TypeNameRead/WriteDescription
AjPVarallthysOutputVariation input stream
void RETURN

From EMBOSS 6.4.0

AjPVarall: Variation input stream casts

These functions return the contents of a variation input stream object

Functions:
ajVarallGetvarIdReturns the identifier of the current variation in an input stream

Function ajVarallGetvarId

Returns the identifier of the current variation in an input stream

Prototype

const AjPStr ajVarallGetvarId (
      const AjPVarall thys
);

TypeNameRead/WriteDescription
const AjPVarallthysInputVariation input stream
const AjPStr RETURNIdentifier

From EMBOSS 6.4.0

AjPVarall: Variation input

These functions use a variation input stream object to read data

Functions:
ajVarallNextParse a variation query into format, access, file and entry

Function ajVarallNext

Parse a variation query into format, access, file and entry

Prototype

AjBool ajVarallNext (
      AjPVarall thys,
      AjPVar* Pvar
);

TypeNameRead/WriteDescription
AjPVarallthysOutputVariation input stream
AjPVar*PvarModifyVariation returned
AjBool RETURNajTrue on success.

From EMBOSS 6.4.0

Datatype: none

Input formats internals

Sections:
castCasts

Section: cast

Values for input formats

Functions:
ajVarinformatTermTests whether a variation data input format term is known
ajVarinformatTestTests whether a named variation data input format is known

Function ajVarinformatTerm

Tests whether a variation data input format term is known

Prototype

AjBool ajVarinformatTerm (
      const AjPStr term
);

TypeNameRead/WriteDescription
const AjPStrtermInputFormat term EDAM ID
AjBool RETURNajTrue if term was accepted

From EMBOSS 6.4.0

Function ajVarinformatTest

Tests whether a named variation data input format is known

Prototype

AjBool ajVarinformatTest (
      const AjPStr format
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat
AjBool RETURNajTrue if format was accepted

From EMBOSS 6.4.0