ajrefseqread.c

Datatypes:
AjPRefseqin Reference sequence input objects
none Miscellaneous
AjPTable Internal call register table
AjPRefseqall Refseq Input Stream
none Input formats

Datatype: AjPRefseqin

Function is for manipulating reference sequence input objects

Sections:
Reference sequence input constructorsConstructors
reference sequence input destructorsDestructors
reference sequence input modifiersModifiers
castsCasts
Reference sequence data inputsInput

AjPRefseqin: Reference sequence input constructors

All constructors return a new reference sequence input object by pointer. It is the responsibility of the user to first destroy any previous reference 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:
ajRefseqinNewCreates a new reference sequence input object.

Function ajRefseqinNew

Creates a new reference sequence input object.

Prototype

AjPRefseqin ajRefseqinNew (
      void
);

TypeNameRead/WriteDescription
AjPRefseqin RETURNNew reference sequence input object.

In release 6.5.0

AjPRefseqin: reference sequence input destructors

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

Functions:
ajRefseqinDelDeletes a reference sequence input object.

Function ajRefseqinDel

Deletes a reference sequence input object.

Prototype

void ajRefseqinDel (
      AjPRefseqin* pthis
);

TypeNameRead/WriteDescription
AjPRefseqin*pthisDeleteReference sequence input
void RETURN

In release 6.5.0

AjPRefseqin: reference sequence input modifiers

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

Functions:
ajRefseqinClearClears a reference sequence input object back to "as new" condition, except for the query list which must be preserved.
ajRefseqinQryCResets a reference sequence input object using a new Universal Query Address
ajRefseqinQrySResets a reference sequence input object using a new Universal Query Address

Function ajRefseqinClear

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

Prototype

void ajRefseqinClear (
      AjPRefseqin thys
);

TypeNameRead/WriteDescription
AjPRefseqinthysOutputReference sequence input
void RETURN

In release 6.5.0

Function ajRefseqinQryC

Resets a reference sequence input object using a new Universal Query Address

Prototype

void ajRefseqinQryC (
      AjPRefseqin thys,
      const char* txt
);

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

In release 6.5.0

Function ajRefseqinQryS

Resets a reference sequence input object using a new Universal Query Address

Prototype

void ajRefseqinQryS (
      AjPRefseqin thys,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPRefseqinthysModifyReference sequence input object.
const AjPStrstrInputQuery
void RETURN

In release 6.5.0

AjPRefseqin: casts

Return values

Functions:
ajRefseqinTraceDebug calls to trace the data in a reference sequence input object.

Function ajRefseqinTrace

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

Prototype

void ajRefseqinTrace (
      const AjPRefseqin thys
);

TypeNameRead/WriteDescription
const AjPRefseqinthysInputReference sequence input object.
void RETURN

In release 6.5.0

AjPRefseqin: Reference sequence data inputs

These functions read the wxyxdesc data provided by the first argument

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

Function ajRefseqinRead

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

Prototype

AjBool ajRefseqinRead (
      AjPRefseqin refseqin,
      AjPRefseq refseq
);

TypeNameRead/WriteDescription
AjPRefseqinrefseqinModifyReference sequence data input definitions
AjPRefseqrefseqOutputReference sequence data returned.
AjBool RETURNajTrue on success.

In release 6.5.0

Datatype: none

Reference sequence input internals

Sections:
PrintCasts
MiscellaneousMiscellaneous
InternalsMiscellaneous

Section: Print

Printing to a file

Functions:
ajRefseqinprintBookReports the internal data structures as a Docbook table
ajRefseqinprintHtmlReports the internal data structures as an HTML table
ajRefseqinprintTextReports the internal data structures
ajRefseqinprintWikiReports the internal data structures as a wiki table

Function ajRefseqinprintBook

Reports the internal data structures as a Docbook table

Prototype

void ajRefseqinprintBook (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

In release 6.5.0

Function ajRefseqinprintHtml

Reports the internal data structures as an HTML table

Prototype

void ajRefseqinprintHtml (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

In release 6.5.0

Function ajRefseqinprintText

Reports the internal data structures

Prototype

void ajRefseqinprintText (
      AjPFile outf,
      AjBool full
);

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

In release 6.5.0

Function ajRefseqinprintWiki

Reports the internal data structures as a wiki table

Prototype

void ajRefseqinprintWiki (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

In release 6.5.0

Section: Miscellaneous

Functions to initialise and clean up internals

Functions:
ajRefseqinExitCleans up reference sequence input internal memory

Function ajRefseqinExit

Cleans up reference sequence input internal memory

Prototype

void ajRefseqinExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

In release 6.5.0

Section: Internals

Functions to return internal values

Functions:
ajRefseqinTypeGetFieldsReturns the list of known field names for ajRefseqinRead
ajRefseqinTypeGetQlinksReturns the listof known query link operators for ajRefseqinRead

Function ajRefseqinTypeGetFields

Returns the list of known field names for ajRefseqinRead

Prototype

const char* ajRefseqinTypeGetFields (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList of field names

In release 6.5.0

Function ajRefseqinTypeGetQlinks

Returns the listof known query link operators for ajRefseqinRead

Prototype

const char* ajRefseqinTypeGetQlinks (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList of field names

In release 6.5.0

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:
ajRefseqaccessGetDbReturns the table in which reference sequence database access details are registered
ajRefseqaccessMethodGetQlinksTests for a named method for refseq data reading returns the known query link operators
ajRefseqaccessMethodGetScopeTests for a named method for reference sequence data reading and returns the scope (entry, query or all).
ajRefseqaccessMethodTestTests for a named method for reference sequence data reading.

Function ajRefseqaccessGetDb

Returns the table in which reference sequence database access details are registered

Prototype

AjPTable ajRefseqaccessGetDb (
      void
);

TypeNameRead/WriteDescription
AjPTable RETURNAccess functions hash table

In release 6.5.0

Function ajRefseqaccessMethodGetQlinks

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

Prototype

const char* ajRefseqaccessMethodGetQlinks (
      const AjPStr method
);

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

In release 6.5.0

Function ajRefseqaccessMethodGetScope

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

Prototype

ajuint ajRefseqaccessMethodGetScope (
      const AjPStr method
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
ajuint RETURNScope flags

In release 6.5.0

Function ajRefseqaccessMethodTest

Tests for a named method for reference sequence data reading.

Prototype

AjBool ajRefseqaccessMethodTest (
      const AjPStr method
);

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

In release 6.5.0

Datatype: AjPRefseqall

Function is for manipulating refseq input stream objects

Sections:
Refseq Input ConstructorsConstructors
Refseq Input Stream DestructorsDestructors
refseq input stream modifiersModifiers
refseq input stream castsCasts
refseq inputInput

AjPRefseqall: Refseq Input Constructors

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

Functions:
ajRefseqallNewCreates a new refseq input stream object.

Function ajRefseqallNew

Creates a new refseq input stream object.

Prototype

AjPRefseqall ajRefseqallNew (
      void
);

TypeNameRead/WriteDescription
AjPRefseqall RETURNNew refseq input stream object.

In release 6.5.0

AjPRefseqall: Refseq Input Stream Destructors

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

Functions:
ajRefseqallDelDeletes a refseq input stream object.

Function ajRefseqallDel

Deletes a refseq input stream object.

Prototype

void ajRefseqallDel (
      AjPRefseqall* pthis
);

TypeNameRead/WriteDescription
AjPRefseqall*pthisDeleteRefseq input stream
void RETURN

In release 6.5.0

AjPRefseqall: refseq input stream modifiers

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

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

Function ajRefseqallClear

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

Prototype

void ajRefseqallClear (
      AjPRefseqall thys
);

TypeNameRead/WriteDescription
AjPRefseqallthysOutputRefseq input stream
void RETURN

In release 6.5.0

AjPRefseqall: refseq input stream casts

These functions return the contents of a refseq input stream object

Functions:
ajRefseqallGetrefseqIdReturns the identifier of the current refseq in an input stream

Function ajRefseqallGetrefseqId

Returns the identifier of the current refseq in an input stream

Prototype

const AjPStr ajRefseqallGetrefseqId (
      const AjPRefseqall thys
);

TypeNameRead/WriteDescription
const AjPRefseqallthysInputRefseq input stream
const AjPStr RETURNIdentifier

In release 6.5.0

AjPRefseqall: refseq input

These functions use a refseq input stream object to read data

Functions:
ajRefseqallNextParse a refseq query into format, access, file and entry

Function ajRefseqallNext

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

Prototype

AjBool ajRefseqallNext (
      AjPRefseqall thys,
      AjPRefseq* Prefseq
);

TypeNameRead/WriteDescription
AjPRefseqallthysOutputRefseq input stream
AjPRefseq*PrefseqModifyRefseq returned
AjBool RETURNajTrue on success.

In release 6.5.0

Datatype: none

Input formats internals

Sections:
castCasts

Section: cast

Values for input formats

Functions:
ajRefseqinformatTermTests whether a reference sequence data input format term is known
ajRefseqinformatTestTests whether a named reference sequence data input format is known

Function ajRefseqinformatTerm

Tests whether a reference sequence data input format term is known

Prototype

AjBool ajRefseqinformatTerm (
      const AjPStr term
);

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

In release 6.5.0

Function ajRefseqinformatTest

Tests whether a named reference sequence data input format is known

Prototype

AjBool ajRefseqinformatTest (
      const AjPStr format
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat
AjBool RETURNajTrue if term was accepted

In release 6.5.0