ajtaxread.c

Datatypes:
AjPTaxin Taxonomy input objects
none Miscellaneous
AjPTable Internal call register table
AjPTaxall Taxon Input Stream
none Input formats

Datatype: AjPTaxin

Function is for manipulating taxonomy input objects

Sections:
Taxonomy input constructorsConstructors
taxonomy input destructorsDestructors
taxonomy input modifiersModifiers
castsCasts
Taxonomy data inputsInput

AjPTaxin: Taxonomy input constructors

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

Functions:
ajTaxinNewCreates a new taxonomy input object.

Function ajTaxinNew

Creates a new taxonomy input object.

Prototype

AjPTaxin ajTaxinNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxin RETURNNew taxonomy input object.

From EMBOSS 6.4.0

AjPTaxin: taxonomy input destructors

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

Functions:
ajTaxinDelDeletes a taxonomy input object.

Function ajTaxinDel

Deletes a taxonomy input object.

Prototype

void ajTaxinDel (
      AjPTaxin* pthis
);

TypeNameRead/WriteDescription
AjPTaxin*pthisDeleteTaxonomy input
void RETURN

From EMBOSS 6.4.0

AjPTaxin: taxonomy input modifiers

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

Functions:
ajTaxinClearClears a taxonomy input object back to "as new" condition, except for the query list which must be preserved.
ajTaxinQryCResets a taxonomy input object using a new Universal Query Address
ajTaxinQrySResets a taxonomy input object using a new Universal Query Address

Function ajTaxinClear

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

Prototype

void ajTaxinClear (
      AjPTaxin thys
);

TypeNameRead/WriteDescription
AjPTaxinthysOutputTaxonomy input
void RETURN

From EMBOSS 6.4.0

Function ajTaxinQryC

Resets a taxonomy input object using a new Universal Query Address

Prototype

void ajTaxinQryC (
      AjPTaxin thys,
      const char* txt
);

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

From EMBOSS 6.4.0

Function ajTaxinQryS

Resets a taxonomy input object using a new Universal Query Address

Prototype

void ajTaxinQryS (
      AjPTaxin thys,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPTaxinthysModifyTaxonomy input object.
const AjPStrstrInputQuery
void RETURN

From EMBOSS 6.4.0

AjPTaxin: casts

Return values

Functions:
ajTaxinTraceDebug calls to trace the data in a taxonomy input object.

Function ajTaxinTrace

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

Prototype

void ajTaxinTrace (
      const AjPTaxin thys
);

TypeNameRead/WriteDescription
const AjPTaxinthysInputTaxonomy input object.
void RETURN

From EMBOSS 6.4.0

AjPTaxin: Taxonomy data inputs

These functions read the wxyxdesc data provided by the first argument

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

Function ajTaxinRead

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

Prototype

AjBool ajTaxinRead (
      AjPTaxin taxin,
      AjPTax tax
);

TypeNameRead/WriteDescription
AjPTaxintaxinModifyTaxonomy data input definitions
AjPTaxtaxOutputTaxonomy data returned.
AjBool RETURNajTrue on success.

From EMBOSS 6.4.0

Datatype: none

Taxonomy input internals

Sections:
PrintCasts
MiscellaneousMiscellaneous
InternalsMiscellaneous

Section: Print

Printing to a file

Functions:
ajTaxinprintBookReports the internal data structures as a Docbook table
ajTaxinprintHtmlReports the internal data structures as an HTML table
ajTaxinprintTextReports the internal data structures
ajTaxinprintWikiReports the internal data structures as a wiki table

Function ajTaxinprintBook

Reports the internal data structures as a Docbook table

Prototype

void ajTaxinprintBook (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Function ajTaxinprintHtml

Reports the internal data structures as an HTML table

Prototype

void ajTaxinprintHtml (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Function ajTaxinprintText

Reports the internal data structures

Prototype

void ajTaxinprintText (
      AjPFile outf,
      AjBool full
);

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

From EMBOSS 6.4.0

Function ajTaxinprintWiki

Reports the internal data structures as a wiki table

Prototype

void ajTaxinprintWiki (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0

Section: Miscellaneous

Functions to initialise and clean up internals

Functions:
ajTaxinExitCleans up taxonomy input internal memory

Function ajTaxinExit

Cleans up taxonomy input internal memory

Prototype

void ajTaxinExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 6.4.0

Section: Internals

Functions to return internal values

Functions:
ajTaxinTypeGetFieldsReturns the list of known field names for ajTaxinRead
ajTaxinTypeGetQlinksReturns the listof known query link operators for ajTaxinRead

Function ajTaxinTypeGetFields

Returns the list of known field names for ajTaxinRead

Prototype

const char* ajTaxinTypeGetFields (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList of field names

From EMBOSS 6.4.0

Function ajTaxinTypeGetQlinks

Returns the listof known query link operators for ajTaxinRead

Prototype

const char* ajTaxinTypeGetQlinks (
      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:
ajTaxaccessGetDbReturns the table in which taxonomy database access details are registered
ajTaxaccessMethodGetQlinksTests for a named method for taxonomy data reading returns the known query link operators
ajTaxaccessMethodGetScopeTests for a named method for taxonomy data reading and returns the scope (entry, query or all).
ajTaxaccessMethodTestTests for a named method for taxonomy data reading.

Function ajTaxaccessGetDb

Returns the table in which taxonomy database access details are registered

Prototype

AjPTable ajTaxaccessGetDb (
      void
);

TypeNameRead/WriteDescription
AjPTable RETURNAccess functions hash table

From EMBOSS 6.4.0

Function ajTaxaccessMethodGetQlinks

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

Prototype

const char* ajTaxaccessMethodGetQlinks (
      const AjPStr method
);

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

From EMBOSS 6.4.0

Function ajTaxaccessMethodGetScope

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

Prototype

ajuint ajTaxaccessMethodGetScope (
      const AjPStr method
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
ajuint RETURNScope flags

From EMBOSS 6.4.0

Function ajTaxaccessMethodTest

Tests for a named method for taxonomy data reading.

Prototype

AjBool ajTaxaccessMethodTest (
      const AjPStr method
);

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

From EMBOSS 6.4.0

Datatype: AjPTaxall

Function is for manipulating taxon input stream objects

Sections:
Taxon Input ConstructorsConstructors
Taxon Input Stream DestructorsDestructors
taxon input stream modifiersModifiers
taxon input stream castsCasts
taxon inputInput

AjPTaxall: Taxon Input Constructors

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

Functions:
ajTaxallNewCreates a new taxon input stream object.

Function ajTaxallNew

Creates a new taxon input stream object.

Prototype

AjPTaxall ajTaxallNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxall RETURNNew taxon input stream object.

From EMBOSS 6.4.0

AjPTaxall: Taxon Input Stream Destructors

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

Functions:
ajTaxallDelDeletes a taxon input stream object.

Function ajTaxallDel

Deletes a taxon input stream object.

Prototype

void ajTaxallDel (
      AjPTaxall* pthis
);

TypeNameRead/WriteDescription
AjPTaxall*pthisDeletetaxon input stream
void RETURN

From EMBOSS 6.4.0

AjPTaxall: taxon input stream modifiers

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

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

Function ajTaxallClear

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

Prototype

void ajTaxallClear (
      AjPTaxall thys
);

TypeNameRead/WriteDescription
AjPTaxallthysOutputTaxon input stream
void RETURN

From EMBOSS 6.4.0

AjPTaxall: taxon input stream casts

These functions return the contents of a taxon input stream object

Functions:
ajTaxallGettaxIdReturns the identifier of the current taxon in an input stream

Function ajTaxallGettaxId

Returns the identifier of the current taxon in an input stream

Prototype

const AjPStr ajTaxallGettaxId (
      const AjPTaxall thys
);

TypeNameRead/WriteDescription
const AjPTaxallthysInputTaxon input stream
const AjPStr RETURNIdentifier

From EMBOSS 6.4.0

AjPTaxall: taxon input

These functions use a taxon input stream object to read data

Functions:
ajTaxallNextParse a taxon query into format, access, file and entry

Function ajTaxallNext

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

Prototype

AjBool ajTaxallNext (
      AjPTaxall thys,
      AjPTax* Ptax
);

TypeNameRead/WriteDescription
AjPTaxallthysOutputTaxon input stream
AjPTax*PtaxModifyTaxon returned
AjBool RETURNajTrue on success.

From EMBOSS 6.4.0

Datatype: none

Input formats internals

Sections:
castCasts

Section: cast

Values for input formats

Functions:
ajTaxinformatTestTests whether a named taxonomy data input format is known

Function ajTaxinformatTest

Tests whether a named taxonomy data input format is known

Prototype

AjBool ajTaxinformatTest (
      const AjPStr format
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat
AjBool RETURNajTrue if formats was accepted

From EMBOSS 6.4.0