ajfeatread.c

Function ajFeattabinNew

Constructor for an empty feature table input object

Synopsis

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

Returns

AjPFeattabin:

Feature table input object

Description

Constructor for an empty feature table input object

Availability

In release 6.4.0

Function ajFeattabinNewSS

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

Synopsis

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Returns

AjPFeattabin:

Feature table input object

Description

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

Availability

In release 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.

Synopsis

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Input & Output

buff:

(Modify)

Buffer containing feature data

Returns

AjPFeattabin:

Feature table input object

Description

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.

Availability

In release 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.

Synopsis

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

Input

fmt:	(Input)	feature format
name:	(Input)	sequence name
type:	(Input)	feature type

Input & Output

buff:

(Modify)

Buffer containing feature data

Returns

AjPFeattabin:

Feature table input object

Description

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.

Availability

In release 6.4.0

Function ajFeattabinDel

Destructor for a feature table input object

Synopsis

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

Output

pthis:

(Delete)

Feature table input object

Returns

void:

No return value

Description

Destructor for a feature table input object

Availability

In release 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.

Synopsis

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

Input & Output

thys:

(Modify)

Sequence input

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajFeattabinSetRange

Set the begin and end range for a feature table

Synopsis

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

Input

fbegin:	(Input)	Begin position
fend:	(Input)	End position

Input & Output

thys:

(Modify)

Feature table input object

Returns

void:

No return value

Description

Set the begin and end range for a feature table

Availability

In release 6.4.0

Function ajFeattabinSetTypeC

Sets the type for feature input

Synopsis

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

Input

type:

(Input)

Feature type "nucleotide" "protein"

Input & Output

thys:

(Modify)

Feature input object

Returns

AjBool:

ajTrue on success

Description

Sets the type for feature input

Availability

In release 6.4.0

Function ajFeattabinSetTypeS

Sets the type for feature input

Synopsis

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

Input

type:

(Input)

Feature type "nucleotide" "protein"

Input & Output

thys:

(Modify)

Feature input object

Returns

AjBool:

ajTrue on success

Description

Sets the type for feature input

Availability

In release 6.4.0

Function ajFeattabinQryC

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

Synopsis

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

Input

txt:

(Input)

Query

Input & Output

thys:

(Modify)

Feature table input object.

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajFeattabinQryS

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

Synopsis

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

Input

str:

(Input)

Query

Input & Output

thys:

(Modify)

Feature table input object.

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajFeattabinRead

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

Synopsis

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

Input & Output

feattabin:	(Modify)	Feature table input
ftable:	(Modify)	Feature table containing the features read in

Returns

AjBool:

True on success

Description

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

Availability

In release 6.4.0

Function ajFeattableNewRead

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

Synopsis

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

Input & Output

ftin:

(Modify)

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

Returns

AjPFeattable:

Pointer to a new feature table containing the features read in

Description

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

Availability

In release 6.4.0

Function ajFeattableNewReadUfo

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

Synopsis

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)

Input

ufo:

(Input)

UFO feature spec

Input & Output

featin:

(Modify)

Feature input object

Returns

AjPFeattable:

Feature table created, (or NULL if failed)

Description

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

Availability

In release 6.4.0

Function ajFeatreadExit

Prints a summary of file usage with debug calls

Cleans up feature table input internal memory

Synopsis

Prototype

void ajFeatreadExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
void		RETURN

Returns

void:

No return value

Description

Prints a summary of file usage with debug calls

Cleans up feature table input internal memory

Availability

In release 6.4.0

Section: Internals

Functions to return internal values

Functions: ajFeattabinTypeGetFields ajFeattabinTypeGetQlinks ajFeatinPrintFormat ajFeatinPrinthtmlFormat ajFeatinPrintbookFormat ajFeatinPrintwikiFormat ajFeattaballNew ajFeattaballDel ajFeattaballClear ajFeattaballGetfeattableId ajFeattaballNext ajFeattabaccessGetDb ajFeattabaccessMethodGetQlinks ajFeattabaccessMethodGetScope ajFeattabaccessMethodTest ajFeattabinformatTerm ajFeattabinformatTest

Function ajFeattabinTypeGetFields

Returns the listof known field names for ajFeatRead

Synopsis

Prototype

const char* ajFeattabinTypeGetFields (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

Returns

const char*:

List of field names

Description

Returns the listof known field names for ajFeatRead

Availability

In release 6.4.0

Function ajFeattabinTypeGetQlinks

Returns the listof known query link operators for ajFeatRead

Synopsis

Prototype

const char* ajFeattabinTypeGetQlinks (
      void
);

Type Name Read/Write Description

const char* RETURN List of field names

Returns

const char*:

List of field names

Description

Returns the listof known query link operators for ajFeatRead

Availability

In release 6.4.0

Function ajFeatinPrintFormat

Reports the internal data structures for input feature formats

Synopsis

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

Input

full:

(Input)

Full report (usually ajFalse)

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the internal data structures for input feature formats

Availability

In release 6.4.0

Function ajFeatinPrinthtmlFormat

Reports the internal data structures for input feature formats

Synopsis

Prototype

void ajFeatinPrinthtmlFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the internal data structures for input feature formats

Availability

In release 6.4.0

Function ajFeatinPrintbookFormat

Reports the input feature format internals in docbook text format

Synopsis

Prototype

void ajFeatinPrintbookFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the input feature format internals in docbook text format

Availability

In release 6.4.0

Function ajFeatinPrintwikiFormat

Reports the input feature format internals in wiki text format

Synopsis

Prototype

void ajFeatinPrintwikiFormat (
      AjPFile outf
);

Type Name Read/Write Description

AjPFile outf Modify Output file

void RETURN

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Reports the input feature format internals in wiki text format

Availability

In release 6.4.0

Function ajFeattaballNew

Creates a new feature input stream object.

Synopsis

Prototype

AjPFeattaball ajFeattaballNew (
      void
);

Type Name Read/Write Description

AjPFeattaball RETURN New feature input stream object.

Returns

AjPFeattaball:

New feature input stream object.

Description

Creates a new feature input stream object.

Availability

In release 6.4.0

Function ajFeattaballDel

Deletes a feature input stream object.

Synopsis

Prototype

void ajFeattaballDel (
      AjPFeattaball* pthis
);

Type Name Read/Write Description

AjPFeattaball* pthis Delete Feature input stream

void RETURN

Output

pthis:

(Delete)

Feature input stream

Returns

void:

No return value

Description

Deletes a feature input stream object.

Availability

In release 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.

Synopsis

Prototype

void ajFeattaballClear (
      AjPFeattaball thys
);

Type Name Read/Write Description

AjPFeattaball thys Output Feature input stream

void RETURN

Output

thys:

(Output)

Feature input stream

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajFeattaballGetfeattableId

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

Synopsis

Prototype

const AjPStr ajFeattaballGetfeattableId (
      const AjPFeattaball thys
);

Type Name Read/Write Description

const AjPFeattaball thys Input Feature input stream

const AjPStr RETURN Identifier

Input

thys:

(Input)

Feature input stream

Returns

const AjPStr:

Identifier

Description

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

Availability

In release 6.4.0

Function ajFeattaballNext

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

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Return the results in the AjPFeattable object but leave the file open for future calls.

Synopsis

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.

Output

thys:

(Output)

Feature input stream

Input & Output

Pfeattable:

(Modify)

Feature table returned

Returns

AjBool:

ajTrue on success.

Description

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

Split at delimiters. Check for the first part as a valid format Check for the remaining first part as a database name or as a file that can be opened. Anything left is an entryname spec.

Return the results in the AjPFeattable object but leave the file open for future calls.

Availability

In release 6.4.0

Function ajFeattabaccessGetDb

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

Synopsis

Prototype

AjPTable ajFeattabaccessGetDb (
      void
);

Type Name Read/Write Description

AjPTable RETURN Access functions hash table

Returns

AjPTable:

Access functions hash table

Description

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

Availability

In release 6.4.0

Function ajFeattabaccessMethodGetQlinks

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

Synopsis

Prototype

const char* ajFeattabaccessMethodGetQlinks (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

const char* RETURN Known link operators

Input

method:

(Input)

Method required.

Returns

const char*:

Known link operators

Description

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

Availability

In release 6.4.0

Function ajFeattabaccessMethodGetScope

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

Synopsis

Prototype

ajuint ajFeattabaccessMethodGetScope (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

ajuint RETURN Scope flags

Input

method:

(Input)

Method required.

Returns

ajuint:

Scope flags

Description

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

Availability

In release 6.4.0

Function ajFeattabaccessMethodTest

Tests for a named method for feature table reading.

Synopsis

Prototype

AjBool ajFeattabaccessMethodTest (
      const AjPStr method
);

Type Name Read/Write Description

const AjPStr method Input Method required.

AjBool RETURN ajTrue on success.

Input

method:

(Input)

Method required.

Returns

AjBool:

ajTrue on success.

Description

Tests for a named method for feature table reading.

Availability

In release 6.4.0

Function ajFeattabinformatTerm

Tests whether a feature table data input format term is known

Synopsis

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

Input

term:

(Input)

Format term EDAM ID

Returns

AjBool:

ajTrue if term was accepted

Description

Tests whether a feature table data input format term is known

Availability

In release 6.4.0

Function ajFeattabinformatTest

Tests whether a named feature table data input format is known

Synopsis

Prototype

AjBool ajFeattabinformatTest (
      const AjPStr format
);

Type Name Read/Write Description

const AjPStr format Input Format

AjBool RETURN ajTrue if format was accepted

Input

format:

(Input)

Format

Returns

AjBool:

ajTrue if format was accepted

Description

Tests whether a named feature table data input format is known

Availability

In release 6.4.0

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

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

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
const AjPStr	method	Input	Method required.
const char*		RETURN	Known link operators

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

ajfeatread.c

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