ajacd.c
Datatypes: none
ACD internals
Sections: initialisation return internals provenance print exit unused
Initialises everything needed for ACD processing.
Functions: ajAcdInit ajAcdInitP
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 passsed 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 passsed as-is by the calling application. |
| argv: | (Input) | Actual arguments as an array of text. |
Returns
Description
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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 ajAcdInitP (
const char* pgm,
ajint argc,
char* const[] argv,
const char* package
);
| 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 passsed 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 |
| 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 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
Description
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
Returns values to the calling program.
Functions: ajAcdGetAlign ajAcdGetArray ajAcdGetBool ajAcdGetCodon ajAcdGetCpdb ajAcdGetDatafile ajAcdGetDirectory ajAcdGetDirectoryName ajAcdGetDirlist ajAcdGetDiscretestates ajAcdGetDiscretestatesSingle ajAcdGetDistances ajAcdGetDistancesSingle ajAcdGetFeat ajAcdGetFeatout ajAcdGetFilelist ajAcdGetFloat ajAcdGetFrequencies ajAcdGetGraph ajAcdGetGraphxy ajAcdGetInfile ajAcdGetInt ajAcdGetList ajAcdGetListSingle ajAcdGetMatrix ajAcdGetMatrixf ajAcdGetOutcodon ajAcdGetOutcpdb ajAcdGetOutdata ajAcdGetOutdir ajAcdGetOutdirName ajAcdGetOutdiscrete ajAcdGetOutdistance ajAcdGetOutfile ajAcdGetOutfileall ajAcdGetOutfreq ajAcdGetOutmatrix ajAcdGetOutmatrixf ajAcdGetOutproperties ajAcdGetOutscop ajAcdGetOuttree ajAcdGetPattern ajAcdGetProperties ajAcdGetRange ajAcdGetRegexp ajAcdGetRegexpSingle ajAcdGetReport ajAcdGetScop ajAcdGetSelect ajAcdGetSelectSingle ajAcdGetSeq ajAcdGetSeqall ajAcdGetSeqout ajAcdGetSeqoutall ajAcdGetSeqoutset ajAcdGetSeqset ajAcdGetSeqsetall ajAcdGetSeqsetallSingle ajAcdGetString ajAcdGetToggle ajAcdGetTree ajAcdGetTreeSingle ajAcdGetValue ajAcdGetValueDefault ajAcdIsUserdefined
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 |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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 |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
);
| 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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
Input
| token: | (Input) | Text token name |
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
Input
| token: | (Input) | Text token name |
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
ajFileDataNew so this just returns the pointer. |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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 |
Input
| token: | (Input) | Text token name |
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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 |
Input
| token: | (Input) | Text token name |
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
Input
| token: | (Input) | Text token name |
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
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
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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. |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
);
| 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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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 |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
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
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
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
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
);
| 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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
);
| Type | Name | Read/Write | Description |
|---|
| const char* | token | Input | Text token name |
| AjPDir | | RETURN | Output directory object |
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
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
);
| 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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
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
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
Tests whether an ACD item has a value set by the user.
Synopsis
Prototype
AjBool ajAcdIsUserdefined (
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.
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
Sets internal values
Functions: 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
);
| 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 "acdlog", "acdpretty", "acdtable", "acdtrace" and
"acdvalid"
Usage
See source code
Example
In preparation
Errors
See source code
Dependencies
See source code
See Also
See other functions in this section
Availability
In release 5.0.0
Functions providing information about the run-time environment
Functions: ajAcdGetCmdline ajAcdGetInputs ajAcdGetProgram
Returns the original command line as qualifiers and values with newline
delimiters
Synopsis
Prototype
const AjPStr ajAcdGetCmdline (
void
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | | RETURN | Commandline with newlines between qualifiers
and parameters |
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
See Also
See other functions in this section
Availability
In release 5.0.0
Returns the user non-default inputs in commandline form
Synopsis
Prototype
const AjPStr ajAcdGetInputs (
void
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | | RETURN | Commandline with newlines between qualifiers
and parameters |
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
See Also
See other functions in this section
Availability
In release 5.0.0
Returns the application (program) name from the ACD definition.
Synopsis
Prototype
const AjPStr ajAcdGetProgram (
void
);
| Type | Name | Read/Write | Description |
|---|
| const AjPStr | | RETURN | Program name |
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
See Also
See other functions in this section
Availability
In release 5.0.0
Functions: ajAcdPrintAppl ajAcdPrintQual ajAcdPrintType
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
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
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
Input & Output
Returns
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
See Also
See other functions in this section
Availability
In release 5.0.0
Functions called on exit
Functions: 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
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
See Also
See other functions in this section
Availability
In release 5.0.0
Functions: 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
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
See Also
See other functions in this section
Availability
In release 5.0.0