ajacd.c

Datatypes: none

Datatype: none

ACD internals

Sections: initialisation return internals print exit unused deprecated edam

Section: initialisation

Initialises everything needed for ACD processing.

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.

Synopsis

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

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

Input

pgm:	(Input)	Application name, used as the name of the ACD file
argc:	(Input)	Number of arguments provided on the command line, usually passed as-is by the calling application.
argv:	(Input)	Actual arguments as an array of text.

Returns

void:

No return value

Description

Availability

In release 6.4.0

Function ajAcdInitPV

Synopsis

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

Input

pgm:	(Input)	Application name, used as the name of the ACD file
argc:	(Input)	Number of arguments provided on the command line, usually passed as-is by the calling application.
argv:	(Input)	Actual arguments as an array of text.
package:	(Input)	Package name, used to find the ACD file
packversion:	(Input)	Package version

Returns

void:

No return value

Description

Availability

In release 6.4.0

Section: return

Returns values to the calling program.

Functions: ajAcdGetAlign ajAcdGetArray ajAcdGetBoolean ajAcdGetCodon ajAcdGetCpdb ajAcdGetDatafile ajAcdGetDirectory ajAcdGetDirectoryName ajAcdGetDirlist ajAcdGetDiscretestates ajAcdGetDiscretestatesSingle ajAcdGetDistances ajAcdGetDistancesSingle ajAcdGetFeatout ajAcdGetFeatures ajAcdGetFeaturesall ajAcdGetFilelist ajAcdGetFloat ajAcdGetFloatDouble ajAcdGetFrequencies ajAcdGetGraph ajAcdGetGraphxy ajAcdGetInfile ajAcdGetInt ajAcdGetIntLong ajAcdGetList ajAcdGetListSingle ajAcdGetMatrix ajAcdGetMatrixf ajAcdGetObo ajAcdGetOboall ajAcdGetOutcodon ajAcdGetOutcpdb ajAcdGetOutdata ajAcdGetOutdir ajAcdGetOutdirName ajAcdGetOutdiscrete ajAcdGetOutdistance ajAcdGetOutfile ajAcdGetOutfileName ajAcdGetOutfreq ajAcdGetOutmatrix ajAcdGetOutmatrixf ajAcdGetOutobo ajAcdGetOutproperties ajAcdGetOutresource ajAcdGetOutscop ajAcdGetOuttaxon ajAcdGetOuttext ajAcdGetOuttree ajAcdGetOuturl ajAcdGetOutvariation ajAcdGetPattern ajAcdGetProperties ajAcdGetRange ajAcdGetRegexp ajAcdGetRegexpSingle ajAcdGetReport ajAcdGetResource ajAcdGetResourceall ajAcdGetScop ajAcdGetSelect ajAcdGetSelectSingle ajAcdGetSeq ajAcdGetSeqall ajAcdGetSeqout ajAcdGetSeqoutall ajAcdGetSeqoutset ajAcdGetSeqset ajAcdGetSeqsetall ajAcdGetSeqsetallSingle ajAcdGetString ajAcdGetTaxon ajAcdGetTaxonall ajAcdGetText ajAcdGetTextall ajAcdGetToggle ajAcdGetTree ajAcdGetTreeSingle ajAcdGetUrl ajAcdGetUrlall ajAcdGetValue ajAcdGetValueDefault ajAcdGetVariation ajAcdGetVariationall ajAcdGetpathC ajAcdGetpathS ajAcdIsUserdefinedC ajAcdIsUserdefinedS

Function 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.

Synopsis

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

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

Input

token:

(Input)

Text token name

Returns

AjPAlign:

Alignment output object. Already opened by ajAlignOpent so this just returns the object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPFloat ajAcdGetArray (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPFloat RETURN Floating point array object

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

Input

token:

(Input)

Text token name

Returns

AjPFloat:

Floating point array object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

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

Input

token:

(Input)

Text token name

Returns

AjBool:

Boolean value from ACD item

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPCod ajAcdGetCodon (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPCod RETURN Codon object.

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

Input

token:

(Input)

Text token name

Returns

AjPCod:

Codon object.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPFile ajAcdGetCpdb (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPFile RETURN Cpdb input file.

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

Input

token:

(Input)

Text token name

Returns

AjPFile:

Cpdb input file.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

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.

Input

token:

(Input)

Text token name

Returns

AjPFile:

File object. The file was already opened by ajDatafileNewInNameS so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function ajAcdGetDirectory

Returns an item of type AjPDir which has been validated as a directory.

Optionally can be forced to have a fully qualified path when returned.

Synopsis

Prototype

AjPDir ajAcdGetDirectory (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPDir RETURN Directory object

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

Input

token:

(Input)

Text token name

Returns

AjPDir:

Directory object

Description

Returns an item of type AjPDir which has been validated as a directory.

Optionally can be forced to have a fully qualified path when returned.

Availability

In release 6.4.0

Function ajAcdGetDirectoryName

Returns an item of type AjPStr which has been validated as a directory name

Optionally can be forced to have a fully qualified path when returned.

Synopsis

Prototype

AjPStr ajAcdGetDirectoryName (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPStr RETURN Directory path

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

Input

token:

(Input)

Text token name

Returns

AjPStr:

Directory path

Description

Returns an item of type AjPStr which has been validated as a directory name

Optionally can be forced to have a fully qualified path when returned.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPList ajAcdGetDirlist (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPList RETURN List of files.

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

Input

token:

(Input)

Text token name

Returns

AjPList:

List of files.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloState*:

Discrete states object. The string was already set by acdSetDiscretestates so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloState:

Discrete states object. The data was already set by acdSetDiscretestates so this just returns the pointer.

Description

Availability

In release 6.4.0

Function 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.

Synopsis

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.

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloDist*:

Distances object. The string was already set by acdSetDistances so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloDist:

Distances object. The string was already set by acdSetDistances so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

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

Input

token:

(Input)

Text token name

Returns

AjPFeattabOut:

Feature Table output object. Already opened by acdSetFeatout so this just returns the object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

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.

Input

token:

(Input)

Text token name

Returns

AjPFeattable:

Feature Table object. The table was already loaded by acdSetFeat so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function ajAcdGetFeaturesall

Returns an input stream of 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.

Synopsis

Prototype

AjPFeattaball ajAcdGetFeaturesall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPFeattaball RETURN Features input stream

Input

token:

(Input)

Text token name

Returns

AjPFeattaball:

Features input stream

Description

Returns an input stream of 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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPList ajAcdGetFilelist (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPList RETURN List of files.

Input

token:

(Input)

Text token name

Returns

AjPList:

List of files.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

float:

Floating point value from ACD item

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

double:

Floating point value from ACD item

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloFreq:

Frequencies object. The string was already set by acdSetFrequencies so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function ajAcdGetGraph

Returns a graph object which hold user graphics options.

Synopsis

Prototype

AjPGraph ajAcdGetGraph (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPGraph RETURN Graph object.

Input

token:

(Input)

Text token name

Returns

AjPGraph:

Graph object.

Description

Returns a graph object which hold user graphics options.

Availability

In release 6.4.0

Function ajAcdGetGraphxy

Returns a graph object which hold user graphics options.

Synopsis

Prototype

AjPGraph ajAcdGetGraphxy (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPGraph RETURN Graph object.

Input

token:

(Input)

Text token name

Returns

AjPGraph:

Graph object.

Description

Returns a graph object which hold user graphics options.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPFile:

File object. The file was already opened by acdSetInfile so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

The ACD item is expected to have the large attribute set to false.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

ajint:

Integer value from ACD item

Description

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.

The ACD item is expected to have the large attribute set to false.

Availability

In release 6.4.0

Function 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.

The ACD item is expected to have the large attribute set to true.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

ajlong:

Integer value from ACD item

Description

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.

The ACD item is expected to have the large attribute set to true.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPStr*:

String array of values with NULL for last element.

Description

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPStr:

String array of values with NULL for last element.

Description

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPMatrix ajAcdGetMatrix (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPMatrix RETURN Matrix object.

Input

token:

(Input)

Text token name

Returns

AjPMatrix:

Matrix object.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPMatrixf ajAcdGetMatrixf (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPMatrixf RETURN Float Matrix object.

Input

token:

(Input)

Text token name

Returns

AjPMatrixf:

Float Matrix object.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPObo ajAcdGetObo (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPObo RETURN Obo term object

Input

token:

(Input)

Text token name

Returns

AjPObo:

Obo term object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPOboall ajAcdGetOboall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPOboall RETURN Obo input stream

Input

token:

(Input)

Text token name

Returns

AjPOboall:

Obo input stream

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function ajAcdGetOutdir

Returns an item of type AjPDirout which has been validated as an output directory.

Optionally can be forced to have a fully qualified path when returned.

Synopsis

Prototype

AjPDirout ajAcdGetOutdir (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPDirout RETURN Output directory object

Input

token:

(Input)

Text token name

Returns

AjPDirout:

Output directory object

Description

Returns an item of type AjPDirout which has been validated as an output directory.

Optionally can be forced to have a fully qualified path when returned.

Availability

In release 6.4.0

Function ajAcdGetOutdirName

Returns an item of type AjPStr which has been validated as an output directory.

Optionally can be forced to have a fully qualified path when returned.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjPStr:

String containing a directory name

Description

Returns an item of type AjPStr which has been validated as an output directory.

Optionally can be forced to have a fully qualified path when returned.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPFile:

File object. The file was already opened by acdSetOutfile so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Synopsis

Prototype

AjPStr ajAcdGetOutfileName (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPStr RETURN Filename.

Input

token:

(Input)

Text token name

Returns

AjPStr:

Filename.

Description

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.

Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPOutfile:

File object. The file was already opened by acdSetOut so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjPPatlistSeq:

Compiled pattern list of sequence patterns. The original pattern string is available through a call to ajAcdGetValue

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloProp:

Properties array. The data was already set by acdSetProperties so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPRange ajAcdGetRange (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPRange RETURN Range object.

Input

token:

(Input)

Text token name

Returns

AjPRange:

Range object.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjPPatlistRegex:

Compiled regular expression pattern. The original pattern string is available through a call to ajAcdGetValue

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjPRegexp:

Compiled regular expression. The original pattern string is available through a call to ajAcdGetValue

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjPReport:

Report output object. Already opened by ajReportOpen so this just returns the object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPResource ajAcdGetResource (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPResource RETURN Data resource object

Input

token:

(Input)

Text token name

Returns

AjPResource:

Data resource object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPResourceall ajAcdGetResourceall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPResourceall RETURN Data resource input stream

Input

token:

(Input)

Text token name

Returns

AjPResourceall:

Data resource input stream

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPFile ajAcdGetScop (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPFile RETURN Scop input file.

Input

token:

(Input)

Text token name

Returns

AjPFile:

Scop input file.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPStr*:

String array of values with NULL as last element.

Description

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPStr:

String array of values with NULL as last element.

Description

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeq:

Sequence object. The sequence was already loaded by acdSetSeq so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqall:

Sequence stream object. The sequence was already loaded by acdSetSeqall so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqout:

Sequence output object. The file was already opened by acdSetSeqout so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqout:

Sequence output object. The file was already opened by acdSetSeqoutall so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqout:

Sequence output object. The file was already opened by acdSetSeqoutset so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqset:

Sequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function ajAcdGetSeqsetall

Returns an item of type Seqset array as defined in a named ACD item. The array is terminated by a NULL.

Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqset*:

Sequence setall object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

Description

Returns an item of type Seqset array as defined in a named ACD item. The array is terminated by a NULL.

Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPSeqset:

Sequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPStr:

String object. The string was already set by acdSetString so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPTax ajAcdGetTaxon (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPTax RETURN Taxon object

Input

token:

(Input)

Text token name

Returns

AjPTax:

Taxon object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPTaxall ajAcdGetTaxonall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPTaxall RETURN Taxon input stream

Input

token:

(Input)

Text token name

Returns

AjPTaxall:

Taxon input stream

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPText ajAcdGetText (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPText RETURN Text object

Input

token:

(Input)

Text token name

Returns

AjPText:

Text object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPTextall ajAcdGetTextall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPTextall RETURN Text input stream

Input

token:

(Input)

Text token name

Returns

AjPTextall:

Text input stream

Description

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.

Availability

In release 6.4.0

Function 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.

Toggle is an AjBool that is used to switch (toggle) other ACD types.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjBool:

Boolean value from ACD item

Description

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.

Toggle is an AjBool that is used to switch (toggle) other ACD types.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloTree*:

Tree object. The data was already set by acdSetTree so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

AjPPhyloTree:

Tree object. The data was already set by acdSetTree so this just returns the pointer.

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPUrl ajAcdGetUrl (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPUrl RETURN URL object

Input

token:

(Input)

Text token name

Returns

AjPUrl:

URL object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPUrlall ajAcdGetUrlall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPUrlall RETURN URL input stream

Input

token:

(Input)

Text token name

Returns

AjPUrlall:

URL input stream

Description

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.

Availability

In release 6.4.0

Function ajAcdGetValue

Returns the string value of any ACD item

Synopsis

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.

Input

token:

(Input)

Text token name

Returns

const AjPStr:

String object. The string was already set by acdSetString so this just returns the pointer.

Description

Returns the string value of any ACD item

Availability

In release 6.4.0

Function ajAcdGetValueDefault

Returns the default value of any ACD item

Synopsis

Prototype

const AjPStr ajAcdGetValueDefault (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

const AjPStr RETURN Default value.

Input

token:

(Input)

Text token name

Returns

const AjPStr:

Default value.

Description

Returns the default value of any ACD item

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPVar ajAcdGetVariation (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPVar RETURN Variation object

Input

token:

(Input)

Text token name

Returns

AjPVar:

Variation object

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype

AjPVarall ajAcdGetVariationall (
      const char* token
);

Type Name Read/Write Description

const char* token Input Text token name

AjPVarall RETURN Variation input stream

Input

token:

(Input)

Text token name

Returns

AjPVarall:

Variation input stream

Description

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.

Availability

In release 6.4.0

Function 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.

Synopsis

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

Input

token:

(Input)

External application name

Returns

const AjPStr:

Executable application name

Description

Availability

In release 6.4.0

Function ajAcdGetpathS

Synopsis

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

Input

strtoken:

(Input)

External application name

Returns

const AjPStr:

Executable application name

Description

Availability

In release 6.4.0

Function ajAcdIsUserdefinedC

Tests whether an ACD item has a value set by the user.

Synopsis

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

Input

token:

(Input)

Text token name

Returns

AjBool:

True if token is not found as an ACD object name

Description

Tests whether an ACD item has a value set by the user.

Availability

In release 6.4.0

Function ajAcdIsUserdefinedS

Tests whether an ACD item has a value set by the user.

Synopsis

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

Input

strtoken:

(Input)

Text token name

Returns

AjBool:

True if token is not found as an ACD object name

Description

Tests whether an ACD item has a value set by the user.

Availability

In release 6.4.0

Section: internals

Sets internal values

Functions: ajAcdSetControl

Function ajAcdSetControl

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

Sets special internal variables to reflect their presence.

Currently these are "acdhelp", "acdlog", "acdpretty", "acdtable", "acdtrace", "acdvalid", "acdverbose", "acdxsd" and "acdnocommandline"

Synopsis

Prototype

AjBool ajAcdSetControl (
      const char* optionName
);

Type Name Read/Write Description

const char* optionName Input option name

AjBool RETURN ajTrue if option was recognised

Input

optionName:

(Input)

option name

Returns

AjBool:

ajTrue if option was recognised

Description

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

Sets special internal variables to reflect their presence.

Currently these are "acdhelp", "acdlog", "acdpretty", "acdtable", "acdtrace", "acdvalid", "acdverbose", "acdxsd" and "acdnocommandline"

Availability

In release 6.4.0

Section: print

Functions: ajAcdPrintAppl ajAcdPrintQual ajAcdPrintType

Function ajAcdPrintAppl

Report details of all known ACD attributes for all applications. For use by EMBOSS entrails.

Synopsis

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

Input

full:

(Input)

Full report - currently no extra details printed

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Report details of all known ACD attributes for all applications. For use by EMBOSS entrails.

Availability

In release 6.4.0

Function ajAcdPrintQual

Report details of all known ACD qualifiers for all applications. For use by EMBOSS entrails.

Synopsis

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

Input

full:

(Input)

Full report - currently no extra details printed

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Report details of all known ACD qualifiers for all applications. For use by EMBOSS entrails.

Availability

In release 6.4.0

Function ajAcdPrintType

Report details of all known ACD types. For use by EMBOSS entrails.

Synopsis

Prototype

void ajAcdPrintType (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full report

void RETURN

Input

full:

(Input)

Full report

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Report details of all known ACD types. For use by EMBOSS entrails.

Availability

In release 6.4.0

Section: exit

Functions called on exit

Functions: ajAcdExit

Function ajAcdExit

Reports any unused ACD values

Cleans up ACD processing internal memory

Synopsis

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

Input

silent:

(Input)

Turn off messages (used when some messages are expected but can be ignored).

Returns

void:

No return value

Description

Reports any unused ACD values

Cleans up ACD processing internal memory

Availability

In release 6.4.0

Section: unused

Functions: ajAcdUnused

Function ajAcdUnused

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

Synopsis

Prototype

void ajAcdUnused (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Section: deprecated

Functions: ajAcdGraphicsInit ajAcdGraphicsInitPV

Function 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.

Synopsis

Prototype

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

Input

pgm:	(Input)	Application name, used as the name of the ACD file
argc:	(Input)	Number of arguments provided on the command line, usually passed as-is by the calling application.
argv:	(Input)	Actual arguments as an array of text.

Returns

void:

No return value

Description

Availability

In release 6.4.0

Function ajAcdGraphicsInitPV

Synopsis

Prototype

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

Input

pgm:	(Input)	Application name, used as the name of the ACD file
argc:	(Input)	Number of arguments provided on the command line, usually passed as-is by the calling application.
argv:	(Input)	Actual arguments as an array of text.
package:	(Input)	Package name, used to find the ACD file
packversion:	(Input)	Package version

Returns

void:

No return value

Description

Availability

In release 6.4.0

Section: edam

Functions: ajAcdedamParse ajAcdtypeGetGroup

Function ajAcdedamParse

Parse an EDAM term from a relations attribute

Synopsis

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

Input

relation:

(Input)

Relation single attribute value

Output

id:	(Output)	EDAM term numeric id
namespace:	(Output)	EDAM term namespace
name:	(Output)	EDAM term name

Returns

AjBool:

True on success

Description

Parse an EDAM term from a relations attribute

Availability

In release 6.4.0

Function ajAcdtypeGetGroup

Return the ACD group for an ACD datatype

Synopsis

Prototype

const char* ajAcdtypeGetGroup (
      const AjPStr type
);

Type Name Read/Write Description

const AjPStr type Input ACD type name

const char* RETURN Group name

Input

type:

(Input)

ACD type name

Returns

const char*:

Group name

Description

Return the ACD group for an ACD datatype

Availability

In release 6.4.0

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

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

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

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

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

ajacd.c

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