ajacd.c

Datatypes:

none	ACD internals

Datatype: none

Sections:

initialisation	Miscellaneous
return	Miscellaneous
internals	Miscellaneous
print	Miscellaneous
exit	Miscellaneous
unused	Miscellaneous
deprecated	Miscellaneous
edam	Miscellaneous

Section: initialisation

Functions:

ajAcdInit	Initialises everything. Reads an ACD (AJAX Command Definition) file prompts the user for any missing information, reads all sequences and other input into local structures which applications can request.
ajAcdInitPV	Initialises everything. Reads an ACD (AJAX Command Definition) file prompts the user for any missing information, reads all sequences and other input into local structures which applications can request.

Function ajAcdInit

Prototype

void ajAcdInit (
      const char* pgm,
      ajint argc,
      char* const[] argv
);

Type	Name	Read/Write	Description
const char*	pgm	Input	Application name, used as the name of the ACD file
ajint	argc	Input	Number of arguments provided on the command line, usually passed as-is by the calling application.
char* const[]	argv	Input	Actual arguments as an array of text.
void		RETURN

From EMBOSS 1.0.0

Function ajAcdInitPV

Prototype

void ajAcdInitPV (
      const char* pgm,
      ajint argc,
      char* const[] argv,
      const char* package,
      const char* packversion
);

Type	Name	Read/Write	Description
const char*	pgm	Input	Application name, used as the name of the ACD file
ajint	argc	Input	Number of arguments provided on the command line, usually passed as-is by the calling application.
char* const[]	argv	Input	Actual arguments as an array of text.
const char*	package	Input	Package name, used to find the ACD file
const char*	packversion	Input	Package version
void		RETURN

From EMBOSS 6.2.0

Section: return

Functions:

ajAcdGetAlign	Returns an item of type Align as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetArray	Returns an item of type array as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetBoolean	Returns an item of type Bool as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetCodon	Returns an item of type Codon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetCpdb	Returns an item of type Cpdb as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetDatafile	Returns an item of type Datafile as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetDirectory	Returns an item of type AjPDir which has been validated as a directory.
ajAcdGetDirectoryName	Returns an item of type AjPStr which has been validated as a directory name
ajAcdGetDirlist	Returns a list of files in a given directory. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetDiscretestates	Returns an item of type Discrete states as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetDiscretestatesSingle	Returns an from an array item of type Discrete states as defined in a named ACD item, which is an array of objects terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetDistances	Returns an item of type Distances as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetDistancesSingle	Returns an item of type Distances as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetFeatout	Returns an item of type FeatOut as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetFeatures	Returns an item of type Features as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetFeaturesall	Returns an input stream of an item of type Features as defined in a named ACD item.
ajAcdGetFilelist	Returns a list of files given a comma-separated list. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetFloat	Returns an item of type Float as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetFloatDouble	Returns an item of type Float as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetFrequencies	Returns an item of type Frequencies as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetGraph	Returns a graph object which hold user graphics options.
ajAcdGetGraphxy	Returns a graph object which hold user graphics options.
ajAcdGetInfile	Returns an item of type file as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetInt	Returns an item of type ajint as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetIntLong	Returns an item of type ajlong as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetList	Returns an item of type List as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetListSingle	Returns a single item from an array of type List as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetMatrix	Returns an item of type Matrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetMatrixf	Returns an item of type Matrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetObo	Returns an item of type Obo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOboall	Returns an input stream of an item of type Obo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutcodon	Returns an item of type Outcodon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutcpdb	Returns an item of type Outcpdb as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutdata	Returns an item of type Outdata as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutdir	Returns an item of type AjPDirout which has been validated as an output directory.
ajAcdGetOutdirName	Returns an item of type AjPStr which has been validated as an output directory.
ajAcdGetOutdiscrete	Returns an item of type Outdiscrete as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutdistance	Returns an item of type Outdistance as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutfile	Returns an item of type Outfile as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutfileName	Returns the filename of an item of type Outfile as defined in a named ACD item. The file is closed and can be reused. If the file had the append attribute set it still has the original contents.
ajAcdGetOutfreq	Returns an item of type Outfreq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutmatrix	Returns an item of type Outmatrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutmatrixf	Returns an item of type Outmatrixf as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutobo	Returns an item of type Outobo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutproperties	Returns an item of type Outproperties as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutresource	Returns an item of type Outresource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutscop	Returns an item of type Outscop as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOuttaxon	Returns an item of type Outtaxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOuttext	Returns an item of type Outtext as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOuttree	Returns an item of type Outtree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOuturl	Returns an item of type Outurl as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetOutvariation	Returns an item of type Outvariation as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetPattern	Returns an item of type Pattern as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetProperties	Returns an item of type Properties as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetRange	Returns an item of type Range as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetRegexp	Returns an item of type Regexp as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetRegexpSingle	Returns an item of type Regexp as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetReport	Returns an item of type Report as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetResource	Returns an item of type resource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetResourceall	Returns an input stream of an item of type Resource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetScop	Returns an item of type Scop as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSelect	Returns an item of type Select as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSelectSingle	Returns one item from an array of type Select as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeq	Returns an item of type Seq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeqall	Returns an item of type Seq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeqout	Returns an item of type Seqout as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeqoutall	Returns an item of type Seqoutall as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeqoutset	Returns an item of type Seqoutset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeqset	Returns an item of type Seqset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetSeqsetall	Returns an item of type Seqset array as defined in a named ACD item. The array is terminated by a NULL.
ajAcdGetSeqsetallSingle	Returns an item of type Seqset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetString	Returns an item of type String as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetTaxon	Returns an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetTaxonall	Returns an input stream of an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetText	Returns an item of type Text as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetTextall	Returns an input stream of an item of type Text as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetToggle	Returns an item of type Toggle as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetTree	Returns an item of type Tree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetTreeSingle	Returns an item of type Tree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetUrl	Returns an item of type URL as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetUrlall	Returns an input stream of an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetValue	Returns the string value of any ACD item
ajAcdGetValueDefault	Returns the default value of any ACD item
ajAcdGetVariation	Returns an item of type Variation as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetVariationall	Returns an input stream of an item of type Variation as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.
ajAcdGetpathC	Returns the full path of an application defined in an external: attribute within the application definition. If the application was defined by an EMBOSS_appname environment variable this will use the substitution made when the external attribute was validated.
ajAcdGetpathS	Returns the full path of an application defined in an external: attribute within the application definition. If the application was defined by an EMBOSS_appname environment variable this will use the substitution made when the external attribute was validated.
ajAcdIsUserdefinedC	Tests whether an ACD item has a value set by the user.
ajAcdIsUserdefinedS	Tests whether an ACD item has a value set by the user.

Function ajAcdGetAlign

Prototype

AjPAlign ajAcdGetAlign (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPAlign		RETURN	Alignment output object. Already opened by ajAlignOpent so this just returns the object

From EMBOSS 2.1.0

Function ajAcdGetArray

Prototype

AjPFloat ajAcdGetArray (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFloat		RETURN	Floating point array object

From EMBOSS 1.0.0

Function ajAcdGetBoolean

Prototype

AjBool ajAcdGetBoolean (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjBool		RETURN	Boolean value from ACD item

From EMBOSS 6.0.0

Function ajAcdGetCodon

Prototype

AjPCod ajAcdGetCodon (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPCod		RETURN	Codon object.

From EMBOSS 1.0.0

Function ajAcdGetCpdb

Prototype

AjPFile ajAcdGetCpdb (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFile		RETURN	Cpdb input file.

From EMBOSS 1.8.0

Function ajAcdGetDatafile

Prototype

AjPFile ajAcdGetDatafile (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFile		RETURN	File object. The file was already opened by ajDatafileNewInNameS so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetDirectory

Prototype

AjPDir ajAcdGetDirectory (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPDir		RETURN	Directory object

From EMBOSS 1.0.0

Function ajAcdGetDirectoryName

Prototype

AjPStr ajAcdGetDirectoryName (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr		RETURN	Directory path

From EMBOSS 2.9.0

Function ajAcdGetDirlist

Prototype

AjPList ajAcdGetDirlist (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPList		RETURN	List of files.

From EMBOSS 1.9.0

Function ajAcdGetDiscretestates

Prototype

AjPPhyloState* ajAcdGetDiscretestates (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloState*		RETURN	Discrete states object. The string was already set by acdSetDiscretestates so this just returns the pointer.

From EMBOSS 2.8.0

Function ajAcdGetDiscretestatesSingle

Prototype

AjPPhyloState ajAcdGetDiscretestatesSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloState		RETURN	Discrete states object. The data was already set by acdSetDiscretestates so this just returns the pointer.

From EMBOSS 4.0.0

Function ajAcdGetDistances

Prototype

AjPPhyloDist* ajAcdGetDistances (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloDist*		RETURN	Distances object. The string was already set by acdSetDistances so this just returns the pointer.

From EMBOSS 2.8.0

Function ajAcdGetDistancesSingle

Prototype

AjPPhyloDist ajAcdGetDistancesSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloDist		RETURN	Distances object. The string was already set by acdSetDistances so this just returns the pointer.

From EMBOSS 5.0.0

Function ajAcdGetFeatout

Prototype

AjPFeattabOut ajAcdGetFeatout (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFeattabOut		RETURN	Feature Table output object. Already opened by acdSetFeatout so this just returns the object

From EMBOSS 1.0.0

Function ajAcdGetFeatures

Prototype

AjPFeattable ajAcdGetFeatures (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFeattable		RETURN	Feature Table object. The table was already loaded by acdSetFeat so this just returns the pointer.

From EMBOSS 6.0.0

Function ajAcdGetFeaturesall

Prototype

AjPFeattaball ajAcdGetFeaturesall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFeattaball		RETURN	Features input stream

From EMBOSS 6.4.0

Function ajAcdGetFilelist

Prototype

AjPList ajAcdGetFilelist (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPList		RETURN	List of files.

From EMBOSS 2.5.0

Function ajAcdGetFloat

Prototype

float ajAcdGetFloat (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
float		RETURN	Floating point value from ACD item

From EMBOSS 1.0.0

Function ajAcdGetFloatDouble

Prototype

double ajAcdGetFloatDouble (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
double		RETURN	Floating point value from ACD item

From EMBOSS 6.1.0

Function ajAcdGetFrequencies

Prototype

AjPPhyloFreq ajAcdGetFrequencies (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloFreq		RETURN	Frequencies object. The string was already set by acdSetFrequencies so this just returns the pointer.

From EMBOSS 2.8.0

Function ajAcdGetGraph

Prototype

AjPGraph ajAcdGetGraph (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPGraph		RETURN	Graph object.

From EMBOSS 1.0.0

Function ajAcdGetGraphxy

Prototype

AjPGraph ajAcdGetGraphxy (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPGraph		RETURN	Graph object.

From EMBOSS 1.0.0

Function ajAcdGetInfile

Prototype

AjPFile ajAcdGetInfile (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFile		RETURN	File object. The file was already opened by acdSetInfile so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetInt

Prototype

ajint ajAcdGetInt (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
ajint		RETURN	Integer value from ACD item

From EMBOSS 1.0.0

Function ajAcdGetIntLong

Prototype

ajlong ajAcdGetIntLong (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
ajlong		RETURN	Integer value from ACD item

From EMBOSS 6.1.0

Function ajAcdGetList

Prototype

AjPStr* ajAcdGetList (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr*		RETURN	String array of values with NULL for last element.

From EMBOSS 1.0.0

Function ajAcdGetListSingle

Prototype

AjPStr ajAcdGetListSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr		RETURN	String array of values with NULL for last element.

From EMBOSS 4.0.0

Function ajAcdGetMatrix

Prototype

AjPMatrix ajAcdGetMatrix (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPMatrix		RETURN	Matrix object.

From EMBOSS 1.0.0

Function ajAcdGetMatrixf

Prototype

AjPMatrixf ajAcdGetMatrixf (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPMatrixf		RETURN	Float Matrix object.

From EMBOSS 1.0.0

Function ajAcdGetObo

Prototype

AjPObo ajAcdGetObo (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPObo		RETURN	Obo term object

From EMBOSS 6.4.0

Function ajAcdGetOboall

Prototype

AjPOboall ajAcdGetOboall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOboall		RETURN	Obo input stream

From EMBOSS 6.4.0

Function ajAcdGetOutcodon

Prototype

AjPOutfile ajAcdGetOutcodon (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutcpdb

Prototype

AjPOutfile ajAcdGetOutcpdb (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutdata

Prototype

AjPOutfile ajAcdGetOutdata (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutdir

Prototype

AjPDirout ajAcdGetOutdir (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPDirout		RETURN	Output directory object

From EMBOSS 2.9.0

Function ajAcdGetOutdirName

Prototype

AjPStr ajAcdGetOutdirName (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr		RETURN	String containing a directory name

From EMBOSS 2.9.0

Function ajAcdGetOutdiscrete

Prototype

AjPOutfile ajAcdGetOutdiscrete (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutdistance

Prototype

AjPOutfile ajAcdGetOutdistance (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutfile

Prototype

AjPFile ajAcdGetOutfile (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFile		RETURN	File object. The file was already opened by acdSetOutfile so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetOutfileName

Prototype

AjPStr ajAcdGetOutfileName (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr		RETURN	Filename.

From EMBOSS 6.3.0

Function ajAcdGetOutfreq

Prototype

AjPOutfile ajAcdGetOutfreq (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutmatrix

Prototype

AjPOutfile ajAcdGetOutmatrix (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutmatrixf

Prototype

AjPOutfile ajAcdGetOutmatrixf (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutobo

Prototype

AjPOutfile ajAcdGetOutobo (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0

Function ajAcdGetOutproperties

Prototype

AjPOutfile ajAcdGetOutproperties (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOutresource

Prototype

AjPOutfile ajAcdGetOutresource (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0

Function ajAcdGetOutscop

Prototype

AjPOutfile ajAcdGetOutscop (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOuttaxon

Prototype

AjPOutfile ajAcdGetOuttaxon (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0

Function ajAcdGetOuttext

Prototype

AjPOutfile ajAcdGetOuttext (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0

Function ajAcdGetOuttree

Prototype

AjPOutfile ajAcdGetOuttree (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0

Function ajAcdGetOuturl

Prototype

AjPOutfile ajAcdGetOuturl (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0

Function ajAcdGetOutvariation

Prototype

AjPOutfile ajAcdGetOutvariation (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPOutfile		RETURN	File object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0

Function ajAcdGetPattern

Prototype

AjPPatlistSeq ajAcdGetPattern (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPatlistSeq		RETURN	Compiled pattern list of sequence patterns. The original pattern string is available through a call to ajAcdGetValue

From EMBOSS 4.0.0

Function ajAcdGetProperties

Prototype

AjPPhyloProp ajAcdGetProperties (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloProp		RETURN	Properties array. The data was already set by acdSetProperties so this just returns the pointer.

From EMBOSS 2.8.0

Function ajAcdGetRange

Prototype

AjPRange ajAcdGetRange (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPRange		RETURN	Range object.

From EMBOSS 1.0.0

Function ajAcdGetRegexp

Prototype

AjPPatlistRegex ajAcdGetRegexp (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPatlistRegex		RETURN	Compiled regular expression pattern. The original pattern string is available through a call to ajAcdGetValue

From EMBOSS 1.0.0

Function ajAcdGetRegexpSingle

Prototype

AjPRegexp ajAcdGetRegexpSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPRegexp		RETURN	Compiled regular expression. The original pattern string is available through a call to ajAcdGetValue

From EMBOSS 4.0.0

Function ajAcdGetReport

Prototype

AjPReport ajAcdGetReport (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPReport		RETURN	Report output object. Already opened by ajReportOpen so this just returns the object

From EMBOSS 2.0.0

Function ajAcdGetResource

Prototype

AjPResource ajAcdGetResource (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPResource		RETURN	Data resource object

From EMBOSS 6.4.0

Function ajAcdGetResourceall

Prototype

AjPResourceall ajAcdGetResourceall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPResourceall		RETURN	Data resource input stream

From EMBOSS 6.4.0

Function ajAcdGetScop

Prototype

AjPFile ajAcdGetScop (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPFile		RETURN	Scop input file.

From EMBOSS 1.8.0

Function ajAcdGetSelect

Prototype

AjPStr* ajAcdGetSelect (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr*		RETURN	String array of values with NULL as last element.

From EMBOSS 1.0.0

Function ajAcdGetSelectSingle

Prototype

AjPStr ajAcdGetSelectSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr		RETURN	String array of values with NULL as last element.

From EMBOSS 4.0.0

Function ajAcdGetSeq

Prototype

AjPSeq ajAcdGetSeq (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeq		RETURN	Sequence object. The sequence was already loaded by acdSetSeq so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetSeqall

Prototype

AjPSeqall ajAcdGetSeqall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqall		RETURN	Sequence stream object. The sequence was already loaded by acdSetSeqall so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetSeqout

Prototype

AjPSeqout ajAcdGetSeqout (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqout		RETURN	Sequence output object. The file was already opened by acdSetSeqout so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetSeqoutall

Prototype

AjPSeqout ajAcdGetSeqoutall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqout		RETURN	Sequence output object. The file was already opened by acdSetSeqoutall so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetSeqoutset

Prototype

AjPSeqout ajAcdGetSeqoutset (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqout		RETURN	Sequence output object. The file was already opened by acdSetSeqoutset so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetSeqset

Prototype

AjPSeqset ajAcdGetSeqset (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqset		RETURN	Sequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetSeqsetall

Prototype

AjPSeqset* ajAcdGetSeqsetall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqset*		RETURN	Sequence setall object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

From EMBOSS 2.8.0

Function ajAcdGetSeqsetallSingle

Prototype

AjPSeqset ajAcdGetSeqsetallSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPSeqset		RETURN	Sequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

From EMBOSS 4.0.0

Function ajAcdGetString

Prototype

AjPStr ajAcdGetString (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPStr		RETURN	String object. The string was already set by acdSetString so this just returns the pointer.

From EMBOSS 1.0.0

Function ajAcdGetTaxon

Prototype

AjPTax ajAcdGetTaxon (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPTax		RETURN	Taxon object

From EMBOSS 6.4.0

Function ajAcdGetTaxonall

Prototype

AjPTaxall ajAcdGetTaxonall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPTaxall		RETURN	Taxon input stream

From EMBOSS 6.4.0

Function ajAcdGetText

Prototype

AjPText ajAcdGetText (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPText		RETURN	Text object

From EMBOSS 6.4.0

Function ajAcdGetTextall

Prototype

AjPTextall ajAcdGetTextall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPTextall		RETURN	Text input stream

From EMBOSS 6.4.0

Function ajAcdGetToggle

Prototype

AjBool ajAcdGetToggle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjBool		RETURN	Boolean value from ACD item

From EMBOSS 2.9.0

Function ajAcdGetTree

Prototype

AjPPhyloTree* ajAcdGetTree (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloTree*		RETURN	Tree object. The data was already set by acdSetTree so this just returns the pointer.

From EMBOSS 2.8.0

Function ajAcdGetTreeSingle

Prototype

AjPPhyloTree ajAcdGetTreeSingle (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPPhyloTree		RETURN	Tree object. The data was already set by acdSetTree so this just returns the pointer.

From EMBOSS 4.0.0

Function ajAcdGetUrl

Prototype

AjPUrl ajAcdGetUrl (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPUrl		RETURN	URL object

From EMBOSS 6.4.0

Function ajAcdGetUrlall

Prototype

AjPUrlall ajAcdGetUrlall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPUrlall		RETURN	URL input stream

From EMBOSS 6.4.0

Function ajAcdGetValue

Prototype

const AjPStr ajAcdGetValue (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
const AjPStr		RETURN	String object. The string was already set by acdSetString so this just returns the pointer.

From EMBOSS 4.0.0

Function ajAcdGetValueDefault

Prototype

const AjPStr ajAcdGetValueDefault (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
const AjPStr		RETURN	Default value.

From EMBOSS 6.0.0

Function ajAcdGetVariation

Prototype

AjPVar ajAcdGetVariation (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPVar		RETURN	Variation object

From EMBOSS 6.4.0

Function ajAcdGetVariationall

Prototype

AjPVarall ajAcdGetVariationall (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjPVarall		RETURN	Variation input stream

From EMBOSS 6.4.0

Function ajAcdGetpathC

Prototype

const AjPStr ajAcdGetpathC (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	External application name
const AjPStr		RETURN	Executable application name

From EMBOSS 6.2.0

Function ajAcdGetpathS

Prototype

const AjPStr ajAcdGetpathS (
      const AjPStr strtoken
);

Type	Name	Read/Write	Description
const AjPStr	strtoken	Input	External application name
const AjPStr		RETURN	Executable application name

From EMBOSS 6.2.0

Function ajAcdIsUserdefinedC

Prototype

AjBool ajAcdIsUserdefinedC (
      const char* token
);

Type	Name	Read/Write	Description
const char*	token	Input	Text token name
AjBool		RETURN	True if token is not found as an ACD object name

From EMBOSS 6.2.0

Function ajAcdIsUserdefinedS

Prototype

AjBool ajAcdIsUserdefinedS (
      const AjPStr strtoken
);

Type	Name	Read/Write	Description
const AjPStr	strtoken	Input	Text token name
AjBool		RETURN	True if token is not found as an ACD object name

From EMBOSS 6.2.0

Section: internals

Functions:

ajAcdSetControl

Sets special qualifiers which were originally provided via the command line.

Function ajAcdSetControl

Prototype

AjBool ajAcdSetControl (
      const char* optionName
);

Type	Name	Read/Write	Description
const char*	optionName	Input	option name
AjBool		RETURN	ajTrue if option was recognised

From EMBOSS 2.7.0

Section: print

Functions:

ajAcdPrintAppl	Report details of all known ACD attributes for all applications. For use by EMBOSS entrails.
ajAcdPrintQual	Report details of all known ACD qualifiers for all applications. For use by EMBOSS entrails.
ajAcdPrintType	Report details of all known ACD types. For use by EMBOSS entrails.

Function ajAcdPrintAppl

Prototype

void ajAcdPrintAppl (
      AjPFile outf,
      AjBool full
);

Type	Name	Read/Write	Description
AjPFile	outf	Modify	Output file
AjBool	full	Input	Full report - currently no extra details printed
void		RETURN

From EMBOSS 4.0.0

Function ajAcdPrintQual

Prototype

void ajAcdPrintQual (
      AjPFile outf,
      AjBool full
);

Type	Name	Read/Write	Description
AjPFile	outf	Modify	Output file
AjBool	full	Input	Full report - currently no extra details printed
void		RETURN

From EMBOSS 2.8.0

Function ajAcdPrintType

Prototype

void ajAcdPrintType (
      AjPFile outf,
      AjBool full
);

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

From EMBOSS 1.0.0

Section: exit

Functions:

ajAcdExit

Reports any unused ACD values

Function ajAcdExit

Prototype

void ajAcdExit (
      AjBool silent
);

Type	Name	Read/Write	Description
AjBool	silent	Input	Turn off messages (used when some messages are expected but can be ignored).
void		RETURN

From EMBOSS 2.4.0

Section: unused

Functions:

ajAcdUnused

Dummy function to catch all unused functions defined in the ajacd source file.

Function ajAcdUnused

Prototype

void ajAcdUnused (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 4.0.0

Section: deprecated

Functions:

ajAcdGraphicsInit	Initialises the graphics then everything else. Reads an ACD (AJAX Command Definition) file, prompts the user for any missing information, reads all sequences and other input into local structures which applications can request. Must be called in each EMBOSS program first.
ajAcdGraphicsInitPV	Initialises the graphics then everything else. Reads an ACD (AJAX Command Definition) file, prompts the user for any missing information, reads all sequences and other input into local structures which applications can request. Must be called in each EMBOSS program first.

Function ajAcdGraphicsInit

Prototype

void ajAcdGraphicsInit (
      const char* pgm,
      ajint argc,
      char* const[] argv
);

Type	Name	Read/Write	Description
const char*	pgm	Input	Application name, used as the name of the ACD file
ajint	argc	Input	Number of arguments provided on the command line, usually passed as-is by the calling application.
char* const[]	argv	Input	Actual arguments as an array of text.
void		RETURN

From EMBOSS 6.2.0

Function ajAcdGraphicsInitPV

Prototype

void ajAcdGraphicsInitPV (
      const char* pgm,
      ajint argc,
      char* const[] argv,
      const char* package,
      const char* packversion
);

Type	Name	Read/Write	Description
const char*	pgm	Input	Application name, used as the name of the ACD file
ajint	argc	Input	Number of arguments provided on the command line, usually passed as-is by the calling application.
char* const[]	argv	Input	Actual arguments as an array of text.
const char*	package	Input	Package name, used to find the ACD file
const char*	packversion	Input	Package version
void		RETURN

From EMBOSS 6.2.0

Section: edam

Functions:

ajAcdedamParse	Parse an EDAM term from a relations attribute
ajAcdtypeGetGroup	Return the ACD group for an ACD datatype

Function ajAcdedamParse

Prototype

AjBool ajAcdedamParse (
      const AjPStr relation,
      AjPStr* id,
      AjPStr* namespace,
      AjPStr* name
);

Type	Name	Read/Write	Description
const AjPStr	relation	Input	Relation single attribute value
AjPStr*	id	Output	EDAM term numeric id
AjPStr*	namespace	Output	EDAM term namespace
AjPStr*	name	Output	EDAM term name
AjBool		RETURN	True on success

From EMBOSS 6.4.0

Function ajAcdtypeGetGroup

Prototype

const char* ajAcdtypeGetGroup (
      const AjPStr type
);

Type	Name	Read/Write	Description
const AjPStr	type	Input	ACD type name
const char*		RETURN	Group name

From EMBOSS 6.4.0