ajfeatread.c


Function ajFeattabinNew

Constructor for an empty feature table input object

Prototype

AjPFeattabin ajFeattabinNew (
      void
);

TypeNameRead/WriteDescription
AjPFeattabin RETURNFeature 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
);

TypeNameRead/WriteDescription
const AjPStrfmtInputfeature format
const AjPStrnameInputsequence name
const char*typeInputfeature type
AjPFeattabin RETURNFeature 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
);

TypeNameRead/WriteDescription
const char*fmtInputfeature format
const AjPStrnameInputsequence name
const char*typeInputfeature type
AjPFilebuffbuffModifyBuffer containing feature data
AjPFeattabin RETURNFeature 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
);

TypeNameRead/WriteDescription
const AjPStrfmtInputfeature format
const AjPStrnameInputsequence name
const char*typeInputfeature type
AjPFilebuffbuffModifyBuffer containing feature data
AjPFeattabin RETURNFeature table input object

From EMBOSS 6.4.0


Function ajFeattabinDel

Destructor for a feature table input object

Prototype

void ajFeattabinDel (
      AjPFeattabin* pthis
);

TypeNameRead/WriteDescription
AjPFeattabin*pthisDeleteFeature 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
);

TypeNameRead/WriteDescription
AjPFeattabinthysModifySequence 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
);

TypeNameRead/WriteDescription
AjPFeattabinthysModifyFeature table input object
ajintfbeginInputBegin position
ajintfendInputEnd position
void RETURN

From EMBOSS 6.4.0


Function ajFeattabinSetTypeC

Sets the type for feature input

Prototype

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

TypeNameRead/WriteDescription
AjPFeattabinthysModifyFeature input object
const char*typeInputFeature type "nucleotide" "protein"
AjBool RETURNajTrue on success

From EMBOSS 6.4.0


Function ajFeattabinSetTypeS

Sets the type for feature input

Prototype

AjBool ajFeattabinSetTypeS (
      AjPFeattabin thys,
      const AjPStr type
);

TypeNameRead/WriteDescription
AjPFeattabinthysModifyFeature input object
const AjPStrtypeInputFeature type "nucleotide" "protein"
AjBool RETURNajTrue 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
);

TypeNameRead/WriteDescription
AjPFeattabinthysModifyFeature table input object.
const char*txtInputQuery
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
);

TypeNameRead/WriteDescription
AjPFeattabinthysModifyFeature table input object.
const AjPStrstrInputQuery
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
);

TypeNameRead/WriteDescription
AjPFeattabinfeattabinModifyFeature table input
AjPFeattableftableModifyFeature table containing the features read in
AjBool RETURNTrue 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
);

TypeNameRead/WriteDescription
AjPFeattabinftinModifySpecifies the external source (file) of the features to be read in
AjPFeattable RETURNPointer 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
);

TypeNameRead/WriteDescription
AjPFeattabinfeatinModifyFeature input object
const AjPStrufoInputUFO feature spec
AjPFeattable RETURNFeature 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
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 6.4.0


Section: Internals

Functions to return internal values

Functions:
ajFeattabinTypeGetFieldsReturns the listof known field names for ajFeatRead
ajFeattabinTypeGetQlinksReturns the listof known query link operators for ajFeatRead
ajFeatinPrintFormatReports the internal data structures for input feature formats
ajFeatinPrinthtmlFormatReports the internal data structures for input feature formats
ajFeatinPrintbookFormatReports the input feature format internals in docbook text format
ajFeatinPrintwikiFormatReports the input feature format internals in wiki text format
ajFeattaballNewCreates a new feature input stream object.
ajFeattaballDelDeletes a feature input stream object.
ajFeattaballClearClears a feature input stream object back to "as new" condition, except for the query list which must be preserved.
ajFeattaballGetfeattableIdReturns the identifier of the current feature table in an input stream
ajFeattaballNextParse a feature query into format, access, file and entry
ajFeattabaccessGetDbreturns the table in which feature table database access details are registered
ajFeattabaccessMethodGetQlinksTests for a named method for feature table term reading and returns the known query link operators
ajFeattabaccessMethodGetScopeTests for a named method for feature table term reading and returns the scope (entry, query or all).
ajFeattabaccessMethodTestTests for a named method for feature table reading.
ajFeattabinformatTermTests whether a feature table data input format term is known
ajFeattabinformatTestTests 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
);

TypeNameRead/WriteDescription
const char* RETURNList of field names

From EMBOSS 6.4.0


Function ajFeattabinTypeGetQlinks

Returns the listof known query link operators for ajFeatRead

Prototype

const char* ajFeattabinTypeGetQlinks (
      void
);

TypeNameRead/WriteDescription
const char* RETURNList 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
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull 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
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput 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
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput 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
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

From EMBOSS 6.4.0


Function ajFeattaballNew

Creates a new feature input stream object.

Prototype

AjPFeattaball ajFeattaballNew (
      void
);

TypeNameRead/WriteDescription
AjPFeattaball RETURNNew feature input stream object.

From EMBOSS 6.4.0


Function ajFeattaballDel

Deletes a feature input stream object.

Prototype

void ajFeattaballDel (
      AjPFeattaball* pthis
);

TypeNameRead/WriteDescription
AjPFeattaball*pthisDeleteFeature 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
);

TypeNameRead/WriteDescription
AjPFeattaballthysOutputFeature 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
);

TypeNameRead/WriteDescription
const AjPFeattaballthysInputFeature input stream
const AjPStr RETURNIdentifier

From EMBOSS 6.4.0


Function ajFeattaballNext

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

Prototype

AjBool ajFeattaballNext (
      AjPFeattaball thys,
      AjPFeattable* Pfeattable
);

TypeNameRead/WriteDescription
AjPFeattaballthysOutputFeature input stream
AjPFeattable*PfeattableModifyFeature table returned
AjBool RETURNajTrue 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
);

TypeNameRead/WriteDescription
AjPTable RETURNAccess 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
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
const char* RETURNKnown 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
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
ajuint RETURNScope flags

From EMBOSS 6.4.0


Function ajFeattabaccessMethodTest

Tests for a named method for feature table reading.

Prototype

AjBool ajFeattabaccessMethodTest (
      const AjPStr method
);

TypeNameRead/WriteDescription
const AjPStrmethodInputMethod required.
AjBool RETURNajTrue 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
);

TypeNameRead/WriteDescription
const AjPStrtermInputFormat term EDAM ID
AjBool RETURNajTrue 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
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat
AjBool RETURNajTrue if format was accepted

From EMBOSS 6.4.0