ajoboread.c

Datatypes:

AjPOboin Obo Input

AjPOboall Obo Input Stream

none Input formats

AjPStr Query string

AjPQuery Obo query objects

AjPOboData Obo Data

AjPStr Obo file line

none Miscellaneous functions

AjPTable Internal call register table

Datatype: AjPOboin

Function is for manipulating obo input objects

Sections:

Obo Input Constructors Constructors

Obo Input Destructors Destructors

obo input modifiers Modifiers

casts Casts

obo term inputs Input

AjPOboin: Obo Input Constructors

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

Functions:

ajOboinNew Creates a new obo input object.

Function ajOboinNew

Creates a new obo input object.

Prototype

AjPOboin ajOboinNew (
      void
);

Type Name Read/Write Description

AjPOboin RETURN New obo input object.

Type	Name	Read/Write	Description
`AjPOboin`		RETURN	New obo input object.

From EMBOSS 6.4.0

AjPOboin: Obo Input Destructors

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

Functions:

ajOboinDel Deletes an obo input object.

Function ajOboinDel

Deletes an obo input object.

Prototype

void ajOboinDel (
      AjPOboin* pthis
);

Type Name Read/Write Description

AjPOboin* pthis Delete Obo input

void RETURN

Type	Name	Read/Write	Description
`AjPOboin*`	`pthis`	Delete	Obo input
`void`		RETURN

From EMBOSS 6.4.0

AjPOboin: obo input modifiers

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

Functions:

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

ajOboinQryC Resets an obo term input object using a new Universal obo term Address

ajOboinQryS Resets an obo term input object using a new Universal obo term Address

Function ajOboinClear

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

Prototype

void ajOboinClear (
      AjPOboin thys
);

Type Name Read/Write Description

AjPOboin thys Output obo term input

void RETURN

Type	Name	Read/Write	Description
`AjPOboin`	`thys`	Output	obo term input
`void`		RETURN

From EMBOSS 6.4.0

Function ajOboinQryC

Resets an obo term input object using a new Universal obo term Address

Prototype

void ajOboinQryC (
      AjPOboin thys,
      const char* txt
);

Type Name Read/Write Description

AjPOboin thys Modify obo term input object.

const char* txt Input Query

void RETURN

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

From EMBOSS 6.4.0

Function ajOboinQryS

Resets an obo term input object using a new Universal obo term Address

Prototype

void ajOboinQryS (
      AjPOboin thys,
      const AjPStr str
);

Type Name Read/Write Description

AjPOboin thys Modify obo term input object.

const AjPStr str Input Query

void RETURN

Type	Name	Read/Write	Description
`AjPOboin`	`thys`	Modify	obo term input object.
`const AjPStr`	`str`	Input	Query
`void`		RETURN

From EMBOSS 6.4.0

AjPOboin: casts

Return values

Functions:

ajOboinGetQryS Returns the query of an obo term input object

ajOboinTrace Debug calls to trace the data in an obo term input object.

Function ajOboinGetQryS

Returns the query of an obo term input object

Prototype

const AjPStr ajOboinGetQryS (
      const AjPOboin thys
);

Type Name Read/Write Description

const AjPOboin thys Input obo term input object.

const AjPStr RETURN Query string

Type	Name	Read/Write	Description
`const AjPOboin`	`thys`	Input	obo term input object.
`const AjPStr`		RETURN	Query string

From EMBOSS 6.4.0

Function ajOboinTrace

Debug calls to trace the data in an obo term input object.

Prototype

void ajOboinTrace (
      const AjPOboin thys
);

Type Name Read/Write Description

const AjPOboin thys Input obo term input object.

void RETURN

Type	Name	Read/Write	Description
`const AjPOboin`	`thys`	Input	obo term input object.
`void`		RETURN

From EMBOSS 6.4.0

AjPOboin: obo term inputs

These functions read the obo term provided by the first argument

Functions:

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

Function ajOboinRead

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

Prototype

AjBool ajOboinRead (
      AjPOboin oboin,
      AjPObo obo
);

Type Name Read/Write Description

AjPOboin oboin Modify obo term input definitions

AjPObo obo Output obo term returned.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPOboin`	`oboin`	Modify	obo term input definitions
`AjPObo`	`obo`	Output	obo term returned.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.4.0

Datatype: AjPOboall

Function is for manipulating obo input stream objects

Sections:

Obo Input Constructors Constructors

OBO Input Stream Destructors Destructors

obo input stream modifiers Modifiers

obo input stream casts Casts

obo input General use

AjPOboall: Obo Input Constructors

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

Functions:

ajOboallNew Creates a new obo input stream object.

Function ajOboallNew

Creates a new obo input stream object.

Prototype

AjPOboall ajOboallNew (
      void
);

Type Name Read/Write Description

AjPOboall RETURN New obo input stream object.

Type	Name	Read/Write	Description
`AjPOboall`		RETURN	New obo input stream object.

From EMBOSS 6.4.0

AjPOboall: OBO Input Stream Destructors

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

Functions:

ajOboallDel Deletes an obo input stream object.

Function ajOboallDel

Deletes an obo input stream object.

Prototype

void ajOboallDel (
      AjPOboall* pthis
);

Type Name Read/Write Description

AjPOboall* pthis Delete Obo input stream

void RETURN

Type	Name	Read/Write	Description
`AjPOboall*`	`pthis`	Delete	Obo input stream
`void`		RETURN

From EMBOSS 6.4.0

AjPOboall: obo input stream modifiers

These functions use the contents of an obo term input stream object and update them.

Functions:

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

Function ajOboallClear

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

Prototype

void ajOboallClear (
      AjPOboall thys
);

Type Name Read/Write Description

AjPOboall thys Output obo term input stream

void RETURN

Type	Name	Read/Write	Description
`AjPOboall`	`thys`	Output	obo term input stream
`void`		RETURN

From EMBOSS 6.4.0

AjPOboall: obo input stream casts

These functions return the contents of an obo term input stream object

Functions:

ajOboallGetQryS Returns the query of an input stream

ajOboallGetoboId Returns the identifier of the current obo term in an input stream

Function ajOboallGetQryS

Returns the query of an input stream

Prototype

const AjPStr ajOboallGetQryS (
      const AjPOboall thys
);

Type Name Read/Write Description

const AjPOboall thys Input obo term input stream

const AjPStr RETURN Identifier

Type	Name	Read/Write	Description
`const AjPOboall`	`thys`	Input	obo term input stream
`const AjPStr`		RETURN	Identifier

From EMBOSS 6.4.0

Function ajOboallGetoboId

Returns the identifier of the current obo term in an input stream

Prototype

const AjPStr ajOboallGetoboId (
      const AjPOboall thys
);

Type Name Read/Write Description

const AjPOboall thys Input obo term input stream

const AjPStr RETURN Identifier

Type	Name	Read/Write	Description
`const AjPOboall`	`thys`	Input	obo term input stream
`const AjPStr`		RETURN	Identifier

From EMBOSS 6.4.0

AjPOboall: obo input

These functions use an obo term input stream object to read data

Functions:

ajOboallNext Parse an OBO query into format, access, file and entry

Function ajOboallNext

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

Prototype

AjBool ajOboallNext (
      AjPOboall thys,
      AjPObo* Pobo
);

Type Name Read/Write Description

AjPOboall thys Output Obo term input stream

AjPObo* Pobo Modify Obo term returned

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPOboall`	`thys`	Output	Obo term input stream
`AjPObo*`	`Pobo`	Modify	Obo term returned
`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:

ajOboinformatTerm tests whether an OBO input format term is known

ajOboinformatTest tests whether a named OBO input format is known

Function ajOboinformatTerm

tests whether an OBO input format term is known

Prototype

AjBool ajOboinformatTerm (
      const AjPStr term
);

Type Name Read/Write Description

const AjPStr term Input Format term EDAM ID

AjBool RETURN ajTrue if term was accepted

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

From EMBOSS 6.4.0

Function ajOboinformatTest

tests whether a named OBO input format is known

Prototype

AjBool ajOboinformatTest (
      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

Datatype: AjPStr

Query string processing

Sections:

Casts Casts

AjPStr: Casts

returns attributes of a query string

Functions:

ajOboqryGetObo Returns an obo term given a query

Function ajOboqryGetObo

Returns an obo term given a query

Prototype

AjBool ajOboqryGetObo (
      const AjPStr qry,
      AjPObo obo
);

Type Name Read/Write Description

const AjPStr qry Input Query

AjPObo obo Modify obo term

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPStr`	`qry`	Input	Query
`AjPObo`	`obo`	Modify	obo term
`AjBool`		RETURN	ajTrue on success

From EMBOSS 6.4.0

Datatype: AjPQuery

Obo query object functions

Sections:

Query Casts Casts

AjPQuery: Query Casts

These functions examine the contents of query object and return some derived information. Some of them provide access to the internal components of a query object. They are provided for programming convenience but should be used with caution.

Functions:

ajOboqueryGetallObofields Returns the standard obo query string from a query

Function ajOboqueryGetallObofields

Returns the standard obo query string from a query

Prototype

ajuint ajOboqueryGetallObofields (
      const AjPQuery query,
      const AjPStr* id,
      const AjPStr* acc,
      const AjPStr* nam,
      const AjPStr* des,
      const AjPStr* up,
      const AjPStr* space
);

Type Name Read/Write Description

const AjPQuery query Input Query

const AjPStr* id Output Id query

const AjPStr* acc Output Accession query

const AjPStr* nam Output Name query

const AjPStr* des Output Description query

const AjPStr* up Output Parent query

const AjPStr* space Output Namespace query

ajuint RETURN Number of fields found

Type	Name	Read/Write	Description
`const AjPQuery`	`query`	Input	Query
`const AjPStr*`	`id`	Output	Id query
`const AjPStr*`	`acc`	Output	Accession query
`const AjPStr*`	`nam`	Output	Name query
`const AjPStr*`	`des`	Output	Description query
`const AjPStr*`	`up`	Output	Parent query
`const AjPStr*`	`space`	Output	Namespace query
`ajuint`		RETURN	Number of fields found

From EMBOSS 6.4.0

Datatype: AjPOboData

Function is for manipulating obo internal data objects

Sections:

constructors Constructors

casts Casts

AjPOboData: constructors

Constructors

Functions:

ajObodataNew Obo data internals constructor

ajObodataParseObofile Parse an OBO format file

Function ajObodataNew

Obo data internals constructor

Prototype

AjPOboData ajObodataNew (
      void
);

Type Name Read/Write Description

AjPOboData RETURN New object

Type	Name	Read/Write	Description
`AjPOboData`		RETURN	New object

From EMBOSS 6.4.0

Function ajObodataParseObofile

Parse an OBO format file

Prototype

AjPOboData ajObodataParseObofile (
      AjPFile obofile,
      const char* validations
);

Type Name Read/Write Description

AjPFile obofile Modify OBO format input file

const char* validations Input Validations to turn on or off

AjPOboData RETURN Ontology data object

Type	Name	Read/Write	Description
`AjPFile`	`obofile`	Modify	OBO format input file
`const char*`	`validations`	Input	Validations to turn on or off
`AjPOboData`		RETURN	Ontology data object

From EMBOSS 6.4.0

AjPOboData: casts

Retrieve data from an obo data opbject

Functions:

ajObodataFetchId Retrieves an OBO term by ID

ajObodataFetchName Retrieves an OBO term by name

Function ajObodataFetchId

Retrieves an OBO term by ID

Prototype

AjPObo ajObodataFetchId (
      const AjPOboData thys,
      const AjPStr query
);

Type Name Read/Write Description

const AjPOboData thys Input Parsed ontology

const AjPStr query Input OBO identifier

AjPObo RETURN OBO term

Type	Name	Read/Write	Description
`const AjPOboData`	`thys`	Input	Parsed ontology
`const AjPStr`	`query`	Input	OBO identifier
`AjPObo`		RETURN	OBO term

From EMBOSS 6.4.0

Function ajObodataFetchName

Retrieves an OBO term by name

Prototype

AjPObo ajObodataFetchName (
      const AjPOboData thys,
      const AjPStr query
);

Type Name Read/Write Description

const AjPOboData thys Input Parsed ontology

const AjPStr query Input OBO name

AjPObo RETURN OBO term

Type	Name	Read/Write	Description
`const AjPOboData`	`thys`	Input	Parsed ontology
`const AjPStr`	`query`	Input	OBO name
`AjPObo`		RETURN	OBO term

From EMBOSS 6.4.0

Datatype: AjPStr

Processing a line from an OBO format file

Sections:

Modifiers Modifiers

AjPStr: Modifiers

Clean up[ the input line

Functions:

ajObolineCutComment Remove comments starting with an unescaped '!'

ajObolineCutDbxref Remove trailing dbxrefs in square braces

ajObolineCutModifier Remove trailing modifiers in curly braces

ajObolineEscape Clean up escaped characters

Function ajObolineCutComment

Remove comments starting with an unescaped '!'

Prototype

AjBool ajObolineCutComment (
      AjPStr* Pline,
      AjPStr* Pcomment
);

Type Name Read/Write Description

AjPStr* Pline Modify Line with possible comment text

AjPStr* Pcomment Modify Comment text

AjBool RETURN True if a comment was found

Type	Name	Read/Write	Description
`AjPStr*`	`Pline`	Modify	Line with possible comment text
`AjPStr*`	`Pcomment`	Modify	Comment text
`AjBool`		RETURN	True if a comment was found

From EMBOSS 6.4.0

Function ajObolineCutDbxref

Remove trailing dbxrefs in square braces

Prototype

AjBool ajObolineCutDbxref (
      AjPStr* Pline,
      AjPStr* Pdbxref
);

Type Name Read/Write Description

AjPStr* Pline Modify Line with possible trailing dbxref text

AjPStr* Pdbxref Modify Dbxref text

AjBool RETURN True if a trailing dbxref was found

Type	Name	Read/Write	Description
`AjPStr*`	`Pline`	Modify	Line with possible trailing dbxref text
`AjPStr*`	`Pdbxref`	Modify	Dbxref text
`AjBool`		RETURN	True if a trailing dbxref was found

From EMBOSS 6.4.0

Function ajObolineCutModifier

Remove trailing modifiers in curly braces

Prototype

AjBool ajObolineCutModifier (
      AjPStr* Pline,
      AjPStr* Pmodifier
);

Type Name Read/Write Description

AjPStr* Pline Modify Line with possible trailing modifier text

AjPStr* Pmodifier Modify Modifier text

AjBool RETURN True if a trailing modifier was found

Type	Name	Read/Write	Description
`AjPStr*`	`Pline`	Modify	Line with possible trailing modifier text
`AjPStr*`	`Pmodifier`	Modify	Modifier text
`AjBool`		RETURN	True if a trailing modifier was found

From EMBOSS 6.4.0

Function ajObolineEscape

Clean up escaped characters

Prototype

AjBool ajObolineEscape (
      AjPStr* Pline
);

Type Name Read/Write Description

AjPStr* Pline Modify Line with possible comment text

AjBool RETURN True if an escaped character was found

Type	Name	Read/Write	Description
`AjPStr*`	`Pline`	Modify	Line with possible comment text
`AjBool`		RETURN	True if an escaped character was found

From EMBOSS 6.4.0

Datatype: none

Functions to initialise and clean up internals

Sections:

Print Casts

Miscellaneous Miscellaneous

Internals Miscellaneous

Section: Print

Printing to a file

Functions:

ajOboinprintBook Reports the internal data structures as a Docbook table

ajOboinprintHtml Reports the internal data structures as an HTML table

ajOboinprintText Reports the internal data structures

ajOboinprintWiki Reports the internal data structures as a wiki table

Function ajOboinprintBook

Reports the internal data structures as a Docbook table

Prototype

void ajOboinprintBook (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

From EMBOSS 6.4.0

Function ajOboinprintHtml

Reports the internal data structures as an HTML table

Prototype

void ajOboinprintHtml (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

From EMBOSS 6.4.0

Function ajOboinprintText

Reports the internal data structures

Prototype

void ajOboinprintText (
      AjPFile outf,
      AjBool full
);

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 ajOboinprintWiki

Reports the internal data structures as a wiki table

Prototype

void ajOboinprintWiki (
      AjPFile outf
);

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:

ajOboinExit Cleans up obo term input internal memory

Function ajOboinExit

Cleans up obo term input internal memory

Prototype

void ajOboinExit (
      void
);

Type Name Read/Write Description

void RETURN

From EMBOSS 6.4.0

Section: Internals

Functions to return internal values

Functions:

ajOboinTypeGetFields Returns the listof known field names for ajOboinRead

ajOboinTypeGetQlinks Returns the listof known query link operators for ajOboinRead

Function ajOboinTypeGetFields

Returns the listof known field names for ajOboinRead

Prototype

const char* ajOboinTypeGetFields (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

From EMBOSS 6.4.0

Function ajOboinTypeGetQlinks

Returns the listof known query link operators for ajOboinRead

Prototype

const char* ajOboinTypeGetQlinks (
      void
);

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:

ajOboaccessGetDb returns the table in which obo database access details are registered

ajOboaccessMethodGetQlinks Tests for a named method for obo term reading and returns the known query link operators

ajOboaccessMethodGetScope Tests for a named method for obo term reading and returns the scope (entry, query or all).

ajOboaccessMethodTest Tests for a named method for obo reading.

Function ajOboaccessGetDb

returns the table in which obo database access details are registered

Prototype

AjPTable ajOboaccessGetDb (
      void
);

Type Name Read/Write Description

AjPTable RETURN Access functions hash table

From EMBOSS 6.4.0

Function ajOboaccessMethodGetQlinks

Tests for a named method for obo term reading and returns the known query link operators

Prototype

const char* ajOboaccessMethodGetQlinks (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

const char* RETURN Known link operators

From EMBOSS 6.4.0

Function ajOboaccessMethodGetScope

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

Prototype

ajuint ajOboaccessMethodGetScope (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

ajuint RETURN Scope flags

From EMBOSS 6.4.0

Function ajOboaccessMethodTest

Tests for a named method for obo reading.

Prototype

AjBool ajOboaccessMethodTest (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

AjBool RETURN ajTrue on success.

From EMBOSS 6.4.0

AjPOboin	Obo Input
AjPOboall	Obo Input Stream
none	Input formats
AjPStr	Query string
AjPQuery	Obo query objects
AjPOboData	Obo Data
AjPStr	Obo file line
none	Miscellaneous functions
AjPTable	Internal call register table

Obo Input Constructors	Constructors
Obo Input Destructors	Destructors
obo input modifiers	Modifiers
casts	Casts
obo term inputs	Input

ajOboinClear	Clears an obo term input object back to "as new" condition, except for the query list which must be preserved.
ajOboinQryC	Resets an obo term input object using a new Universal obo term Address
ajOboinQryS	Resets an obo term input object using a new Universal obo term Address

ajOboinGetQryS	Returns the query of an obo term input object
ajOboinTrace	Debug calls to trace the data in an obo term input object.

Obo Input Constructors	Constructors
OBO Input Stream Destructors	Destructors
obo input stream modifiers	Modifiers
obo input stream casts	Casts
obo input	General use

ajOboallGetQryS	Returns the query of an input stream
ajOboallGetoboId	Returns the identifier of the current obo term in an input stream

ajOboinformatTerm	tests whether an OBO input format term is known
ajOboinformatTest	tests whether a named OBO input format is known

ajObodataNew	Obo data internals constructor
ajObodataParseObofile	Parse an OBO format file

ajObodataFetchId	Retrieves an OBO term by ID
ajObodataFetchName	Retrieves an OBO term by name

ajObolineCutComment	Remove comments starting with an unescaped '!'
ajObolineCutDbxref	Remove trailing dbxrefs in square braces
ajObolineCutModifier	Remove trailing modifiers in curly braces
ajObolineEscape	Clean up escaped characters

ajOboinprintBook	Reports the internal data structures as a Docbook table
ajOboinprintHtml	Reports the internal data structures as an HTML table
ajOboinprintText	Reports the internal data structures
ajOboinprintWiki	Reports the internal data structures as a wiki table

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`AjBool`	`full`	Input	Full report (usually ajFalse)
`void`		RETURN

ajOboinTypeGetFields	Returns the listof known field names for ajOboinRead
ajOboinTypeGetQlinks	Returns the listof known query link operators for ajOboinRead

ajOboaccessGetDb	returns the table in which obo database access details are registered
ajOboaccessMethodGetQlinks	Tests for a named method for obo term reading and returns the known query link operators
ajOboaccessMethodGetScope	Tests for a named method for obo term reading and returns the scope (entry, query or all).
ajOboaccessMethodTest	Tests for a named method for obo reading.

Type	Name	Read/Write	Description
`const AjPStr`	`method`	Input	Method required.
`const char*`		RETURN	Known link operators