ajfeatread.c

Function ajFeattabinNew

Constructor for an empty feature table input object

Prototype

AjPFeattabin ajFeattabinNew (
      void
);

Type Name Read/Write Description

AjPFeattabin RETURN Feature table input object

Type	Name	Read/Write	Description
`AjPFeattabin`		RETURN	Feature table input object

From EMBOSS 6.4.0

Function ajFeattabinNewSS

Constructor for an empty feature table input object. The format and name are read.

Prototype

AjPFeattabin ajFeattabinNewSS (
      const AjPStr fmt,
      const AjPStr name,
      const char* type
);

Type Name Read/Write Description

const AjPStr fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFeattabin RETURN Feature table input object

Type	Name	Read/Write	Description
`const AjPStr`	`fmt`	Input	feature format
`const AjPStr`	`name`	Input	sequence name
`const char*`	`type`	Input	feature type
`AjPFeattabin`		RETURN	Feature table input object

From EMBOSS 6.4.0

Function ajFeattabinNewCSF

Constructor for an empty feature table input object. The format and name are read. The file buffer is moved to the feature table input object and should not be deleted by the calling program.

Prototype

AjPFeattabin ajFeattabinNewCSF (
      const char* fmt,
      const AjPStr name,
      const char* type,
      AjPFilebuff buff
);

Type Name Read/Write Description

const char* fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFilebuff buff Modify Buffer containing feature data

AjPFeattabin RETURN Feature table input object

Type	Name	Read/Write	Description
`const char*`	`fmt`	Input	feature format
`const AjPStr`	`name`	Input	sequence name
`const char*`	`type`	Input	feature type
`AjPFilebuff`	`buff`	Modify	Buffer containing feature data
`AjPFeattabin`		RETURN	Feature table input object

From EMBOSS 6.4.0

Function ajFeattabinNewSSF

Constructor for an empty feature table input object. The format and name are read. The file buffer is moved to the feature table input object and should not be deleted by the calling program.

Prototype

AjPFeattabin ajFeattabinNewSSF (
      const AjPStr fmt,
      const AjPStr name,
      const char* type,
      AjPFilebuff buff
);

Type Name Read/Write Description

const AjPStr fmt Input feature format

const AjPStr name Input sequence name

const char* type Input feature type

AjPFilebuff buff Modify Buffer containing feature data

AjPFeattabin RETURN Feature table input object

Type	Name	Read/Write	Description
`const AjPStr`	`fmt`	Input	feature format
`const AjPStr`	`name`	Input	sequence name
`const char*`	`type`	Input	feature type
`AjPFilebuff`	`buff`	Modify	Buffer containing feature data
`AjPFeattabin`		RETURN	Feature table input object

From EMBOSS 6.4.0

Function ajFeattabinDel

Destructor for a feature table input object

Prototype

void ajFeattabinDel (
      AjPFeattabin* pthis
);

Type Name Read/Write Description

AjPFeattabin* pthis Delete Feature table input object

void RETURN

Type	Name	Read/Write	Description
`AjPFeattabin*`	`pthis`	Delete	Feature table input object
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattabinClear

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

Prototype

void ajFeattabinClear (
      AjPFeattabin thys
);

Type Name Read/Write Description

AjPFeattabin thys Modify Sequence input

void RETURN

Type	Name	Read/Write	Description
`AjPFeattabin`	`thys`	Modify	Sequence input
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattabinSetRange

Set the begin and end range for a feature table

Prototype

void ajFeattabinSetRange (
      AjPFeattabin thys,
      ajint fbegin,
      ajint fend
);

Type Name Read/Write Description

AjPFeattabin thys Modify Feature table input object

ajint fbegin Input Begin position

ajint fend Input End position

void RETURN

Type	Name	Read/Write	Description
`AjPFeattabin`	`thys`	Modify	Feature table input object
`ajint`	`fbegin`	Input	Begin position
`ajint`	`fend`	Input	End position
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattabinSetTypeC

Sets the type for feature input

Prototype

AjBool ajFeattabinSetTypeC (
      AjPFeattabin thys,
      const char* type
);

Type Name Read/Write Description

AjPFeattabin thys Modify Feature input object

const char* type Input Feature type "nucleotide" "protein"

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFeattabin`	`thys`	Modify	Feature input object
`const char*`	`type`	Input	Feature type "nucleotide" "protein"
`AjBool`		RETURN	ajTrue on success

From EMBOSS 6.4.0

Function ajFeattabinSetTypeS

Sets the type for feature input

Prototype

AjBool ajFeattabinSetTypeS (
      AjPFeattabin thys,
      const AjPStr type
);

Type Name Read/Write Description

AjPFeattabin thys Modify Feature input object

const AjPStr type Input Feature type "nucleotide" "protein"

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFeattabin`	`thys`	Modify	Feature input object
`const AjPStr`	`type`	Input	Feature type "nucleotide" "protein"
`AjBool`		RETURN	ajTrue on success

From EMBOSS 6.4.0

Function ajFeattabinQryC

Resets a feature table input object using a new Universal Query Address

Prototype

void ajFeattabinQryC (
      AjPFeattabin thys,
      const char* txt
);

Type Name Read/Write Description

AjPFeattabin thys Modify Feature table input object.

const char* txt Input Query

void RETURN

Type	Name	Read/Write	Description
`AjPFeattabin`	`thys`	Modify	Feature table input object.
`const char*`	`txt`	Input	Query
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattabinQryS

Resets a feature table input object using a new Universal Query Address

Prototype

void ajFeattabinQryS (
      AjPFeattabin thys,
      const AjPStr str
);

Type Name Read/Write Description

AjPFeattabin thys Modify Feature table input object.

const AjPStr str Input Query

void RETURN

Type	Name	Read/Write	Description
`AjPFeattabin`	`thys`	Modify	Feature table input object.
`const AjPStr`	`str`	Input	Query
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattabinRead

Generic interface function for reading in features from a file given the file handle.

Prototype

AjBool ajFeattabinRead (
      AjPFeattabin feattabin,
      AjPFeattable ftable
);

Type Name Read/Write Description

AjPFeattabin feattabin Modify Feature table input

AjPFeattable ftable Modify Feature table containing the features read in

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFeattabin`	`feattabin`	Modify	Feature table input
`AjPFeattable`	`ftable`	Modify	Feature table containing the features read in
`AjBool`		RETURN	True on success

From EMBOSS 6.4.0

Function ajFeattableNewRead

Generic interface function for reading in features from a file given the file handle.

Prototype

AjPFeattable ajFeattableNewRead (
      AjPFeattabin ftin
);

Type Name Read/Write Description

AjPFeattabin ftin Modify Specifies the external source (file) of the features to be read in

AjPFeattable RETURN Pointer to a new feature table containing the features read in

Type	Name	Read/Write	Description
`AjPFeattabin`	`ftin`	Modify	Specifies the external source (file) of the features to be read in
`AjPFeattable`		RETURN	Pointer to a new feature table containing the features read in

From EMBOSS 6.2.0

Function ajFeattableNewReadUfo

Parses a UFO, opens an input file, and reads a feature table

Prototype

AjPFeattable ajFeattableNewReadUfo (
      AjPFeattabin featin,
      const AjPStr ufo
);

Type Name Read/Write Description

AjPFeattabin featin Modify Feature input object

const AjPStr ufo Input UFO feature spec

AjPFeattable RETURN Feature table created, (or NULL if failed)

Type	Name	Read/Write	Description
`AjPFeattabin`	`featin`	Modify	Feature input object
`const AjPStr`	`ufo`	Input	UFO feature spec
`AjPFeattable`		RETURN	Feature table created, (or NULL if failed)

From EMBOSS 6.2.0

Function ajFeatreadExit

Prints a summary of file usage with debug calls

Prototype

void ajFeatreadExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.4.0

Section: Internals

Functions to return internal values

Functions:

ajFeattabinTypeGetFields Returns the listof known field names for ajFeatRead

ajFeattabinTypeGetQlinks Returns the listof known query link operators for ajFeatRead

ajFeatinPrintFormat Reports the internal data structures for input feature formats

ajFeatinPrinthtmlFormat Reports the internal data structures for input feature formats

ajFeatinPrintbookFormat Reports the input feature format internals in docbook text format

ajFeatinPrintwikiFormat Reports the input feature format internals in wiki text format

ajFeattaballNew Creates a new feature input stream object.

ajFeattaballDel Deletes a feature input stream object.

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

ajFeattaballGetfeattableId Returns the identifier of the current feature table in an input stream

ajFeattaballNext Parse a feature query into format, access, file and entry

ajFeattabaccessGetDb returns the table in which feature table database access details are registered

ajFeattabaccessMethodGetQlinks Tests for a named method for feature table term reading and returns the known query link operators

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

ajFeattabaccessMethodTest Tests for a named method for feature table reading.

ajFeattabinformatTerm Tests whether a feature table data input format term is known

ajFeattabinformatTest Tests whether a named feature table data input format is known

Function ajFeattabinTypeGetFields

Returns the listof known field names for ajFeatRead

Prototype

const char* ajFeattabinTypeGetFields (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

Type	Name	Read/Write	Description
`const char*`		RETURN	List of field names

From EMBOSS 6.4.0

Function ajFeattabinTypeGetQlinks

Returns the listof known query link operators for ajFeatRead

Prototype

const char* ajFeattabinTypeGetQlinks (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

Type	Name	Read/Write	Description
`const char*`		RETURN	List of field names

From EMBOSS 6.4.0

Function ajFeatinPrintFormat

Reports the internal data structures for input feature formats

Prototype

void ajFeatinPrintFormat (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full report (usually ajFalse)

void RETURN

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 ajFeatinPrinthtmlFormat

Reports the internal data structures for input feature formats

Prototype

void ajFeatinPrinthtmlFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeatinPrintbookFormat

Reports the input feature format internals in docbook text format

Prototype

void ajFeatinPrintbookFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeatinPrintwikiFormat

Reports the input feature format internals in wiki text format

Prototype

void ajFeatinPrintwikiFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattaballNew

Creates a new feature input stream object.

Prototype

AjPFeattaball ajFeattaballNew (
      void
);

Type Name Read/Write Description

AjPFeattaball RETURN New feature input stream object.

Type	Name	Read/Write	Description
`AjPFeattaball`		RETURN	New feature input stream object.

From EMBOSS 6.4.0

Function ajFeattaballDel

Deletes a feature input stream object.

Prototype

void ajFeattaballDel (
      AjPFeattaball* pthis
);

Type Name Read/Write Description

AjPFeattaball* pthis Delete Feature input stream

void RETURN

Type	Name	Read/Write	Description
`AjPFeattaball*`	`pthis`	Delete	Feature input stream
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattaballClear

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

Prototype

void ajFeattaballClear (
      AjPFeattaball thys
);

Type Name Read/Write Description

AjPFeattaball thys Output Feature input stream

void RETURN

Type	Name	Read/Write	Description
`AjPFeattaball`	`thys`	Output	Feature input stream
`void`		RETURN

From EMBOSS 6.4.0

Function ajFeattaballGetfeattableId

Returns the identifier of the current feature table in an input stream

Prototype

const AjPStr ajFeattaballGetfeattableId (
      const AjPFeattaball thys
);

Type Name Read/Write Description

const AjPFeattaball thys Input Feature input stream

const AjPStr RETURN Identifier

Type	Name	Read/Write	Description
`const AjPFeattaball`	`thys`	Input	Feature input stream
`const AjPStr`		RETURN	Identifier

From EMBOSS 6.4.0

Function ajFeattaballNext

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

Prototype

AjBool ajFeattaballNext (
      AjPFeattaball thys,
      AjPFeattable* Pfeattable
);

Type Name Read/Write Description

AjPFeattaball thys Output Feature input stream

AjPFeattable* Pfeattable Modify Feature table returned

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`AjPFeattaball`	`thys`	Output	Feature input stream
`AjPFeattable*`	`Pfeattable`	Modify	Feature table returned
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.4.0

Function ajFeattabaccessGetDb

returns the table in which feature table database access details are registered

Prototype

AjPTable ajFeattabaccessGetDb (
      void
);

Type Name Read/Write Description

AjPTable RETURN Access functions hash table

Type	Name	Read/Write	Description
`AjPTable`		RETURN	Access functions hash table

From EMBOSS 6.4.0

Function ajFeattabaccessMethodGetQlinks

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

Prototype

const char* ajFeattabaccessMethodGetQlinks (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

const char* RETURN Known link operators

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

From EMBOSS 6.4.0

Function ajFeattabaccessMethodGetScope

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

Prototype

ajuint ajFeattabaccessMethodGetScope (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

ajuint RETURN Scope flags

Type	Name	Read/Write	Description
`const AjPStr`	`method`	Input	Method required.
`ajuint`		RETURN	Scope flags

From EMBOSS 6.4.0

Function ajFeattabaccessMethodTest

Tests for a named method for feature table reading.

Prototype

AjBool ajFeattabaccessMethodTest (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

AjBool RETURN ajTrue on success.

Type	Name	Read/Write	Description
`const AjPStr`	`method`	Input	Method required.
`AjBool`		RETURN	ajTrue on success.

From EMBOSS 6.4.0

Function ajFeattabinformatTerm

Tests whether a feature table data input format term is known

Prototype

AjBool ajFeattabinformatTerm (
      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 ajFeattabinformatTest

Tests whether a named feature table data input format is known

Prototype

AjBool ajFeattabinformatTest (
      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

ajFeattabinTypeGetFields	Returns the listof known field names for ajFeatRead
ajFeattabinTypeGetQlinks	Returns the listof known query link operators for ajFeatRead
ajFeatinPrintFormat	Reports the internal data structures for input feature formats
ajFeatinPrinthtmlFormat	Reports the internal data structures for input feature formats
ajFeatinPrintbookFormat	Reports the input feature format internals in docbook text format
ajFeatinPrintwikiFormat	Reports the input feature format internals in wiki text format
ajFeattaballNew	Creates a new feature input stream object.
ajFeattaballDel	Deletes a feature input stream object.
ajFeattaballClear	Clears a feature input stream object back to "as new" condition, except for the query list which must be preserved.
ajFeattaballGetfeattableId	Returns the identifier of the current feature table in an input stream
ajFeattaballNext	Parse a feature query into format, access, file and entry
ajFeattabaccessGetDb	returns the table in which feature table database access details are registered
ajFeattabaccessMethodGetQlinks	Tests for a named method for feature table term reading and returns the known query link operators
ajFeattabaccessMethodGetScope	Tests for a named method for feature table term reading and returns the scope (entry, query or all).
ajFeattabaccessMethodTest	Tests for a named method for feature table reading.
ajFeattabinformatTerm	Tests whether a feature table data input format term is known
ajFeattabinformatTest	Tests whether a named feature table data input format is known