ajacd.c

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
);

Input

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

Returns

void:

No return value

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdInitP

Synopsis

Prototype

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

Input

pgm:	(Input)	Application name, used as the name of the ACD file
argc:	(Input)	Number of arguments provided on the command line, usually passsed 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

Returns

void:

No return value

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

return

Defines an ACD variable. DE DE Called when a "variable" type ACD item is checked. Should not be called DE for any other item. DE DE At present there is nothing to prompt for here, though there could DE be, for example, a report of what the program does which would appear DE before any user prompts.

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetBool

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 ajAcdGetBool (
      const char* token
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

Input

token:

(Input)

Text token name

Returns

AjPFile:

File object. The file was already opened by ajFileDataNew 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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetFeat

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 ajAcdGetFeat (
      const char* token
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetGraph

Returns a graph object which hold user graphics options.

Synopsis

Prototype

AjPGraph ajAcdGetGraph (
      const char* token
);

Input

token:

(Input)

Text token name

Returns

AjPGraph:

Graph object.

Description

Returns a graph object which hold user graphics options.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetGraphxy

Returns a graph object which hold user graphics options.

Synopsis

Prototype

AjPGraph ajAcdGetGraphxy (
      const char* token
);

Input

token:

(Input)

Text token name

Returns

AjPGraph:

Graph object.

Description

Returns a graph object which hold user graphics options.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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 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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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.

Synopsis

Prototype

ajint ajAcdGetInt (
      const char* token
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

Input

token:

(Input)

Text token name

Returns

AjPStr*:

String array of values with NULL for last element.

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

Input

token:

(Input)

Text token name

Returns

AjPStr:

String array of values with NULL for last element.

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetOutdir

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

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

Synopsis

Prototype

AjPDir ajAcdGetOutdir (
      const char* token
);

Input

token:

(Input)

Text token name

Returns

AjPDir:

Output directory object

Description

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

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetOutfileall

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 ajAcdGetOutfileall (
      const char* token
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

Input

token:

(Input)

Text token name

Returns

AjPStr*:

String array of values with NULL as last element.

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

Input

token:

(Input)

Text token name

Returns

AjPStr:

String array of values with NULL as last element.

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetSeqsetall

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* ajAcdGetSeqsetall (
      const char* token
);

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 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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetValue

Returns the string value of any ACD item

Synopsis

Prototype

const AjPStr ajAcdGetValue (
      const char* token
);

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

internals

Sets internal values

Function ajAcdSetControl

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

Sets special internal variables to reflect their presence.

Currently these are "acdlog", "acdpretty", "acdtable", "acdtrace" and "acdvalid"

Synopsis

Prototype

AjBool ajAcdSetControl (
      const char* optionName
);

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 "acdlog", "acdpretty", "acdtable", "acdtrace" and "acdvalid"

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

provenance

Functions providing information about the run-time environment

Function ajAcdGetCmdline

Returns the original command line as qualifiers and values with newline delimiters

Synopsis

Prototype

const AjPStr ajAcdGetCmdline (
      void
);

Returns

const AjPStr:

Commandline with newlines between qualifiers and parameters

Description

Returns the original command line as qualifiers and values with newline delimiters

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetInputs

Returns the user non-default inputs in commandline form

Synopsis

Prototype

const AjPStr ajAcdGetInputs (
      void
);

Returns

const AjPStr:

Commandline with newlines between qualifiers and parameters

Description

Returns the user non-default inputs in commandline form

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdGetProgram

Returns the application (program) name from the ACD definition.

Synopsis

Prototype

const AjPStr ajAcdGetProgram (
      void
);

Returns

const AjPStr:

Program name

Description

Returns the application (program) name from the ACD definition.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

print

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
);

Input

full:

(Input)

Full report

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

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
);

Input

full:

(Input)

Full report

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

Function ajAcdPrintType

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

Synopsis

Prototype

void ajAcdPrintType (
      AjPFile outf,
      AjBool full
);

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

exit

Functions called on exit

Function ajAcdExit

Reports any unused ACD values

Cleans up ACD processing internal memory

Synopsis

Prototype

void ajAcdExit (
      AjBool silent
);

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

unused

Function ajAcdUnused

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

Synopsis

Prototype

void ajAcdUnused (
      void
);

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 3.0.0

ajacd.c

Synopsis

Prototype

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Example

Errors

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See Also

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