Datatypes:
none | ACD internals |
Sections:
initialisation | Miscellaneous |
return | Miscellaneous |
internals | Miscellaneous |
Miscellaneous | |
exit | Miscellaneous |
unused | Miscellaneous |
edam | Miscellaneous |
Functions:
ajAcdInit | Initialises everything. Reads an ACD (AJAX Command Definition) file prompts the user for any missing information, reads all sequences and other input into local structures which applications can request. |
ajAcdInitPV | Initialises everything. Reads an ACD (AJAX Command Definition) file prompts the user for any missing information, reads all sequences and other input into local structures which applications can request. |
void ajAcdInit ( const char* pgm, ajint argc, char* const[] argv );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | pgm | Input | Application name, used as the name of the ACD file |
ajint | argc | Input | Number of arguments provided on the command line, usually passed as-is by the calling application. |
char* const[] | argv | Input | Actual arguments as an array of text. |
void | RETURN |
From EMBOSS 1.0.0
void ajAcdInitPV ( const char* pgm, ajint argc, char* const[] argv, const char* package, const char* packversion );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | pgm | Input | Application name, used as the name of the ACD file |
ajint | argc | Input | Number of arguments provided on the command line, usually passed as-is by the calling application. |
char* const[] | argv | Input | Actual arguments as an array of text. |
const char* | package | Input | Package name, used to find the ACD file |
const char* | packversion | Input | Package version |
void | RETURN |
From EMBOSS 6.2.0
Functions:
ajAcdGetAlign | Returns an item of type Align as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetArray | Returns an item of type array as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetAssembly | Returns an item of type assembly as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetBoolean | Returns an item of type Bool as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetCodon | Returns an item of type Codon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetCpdb | Returns an item of type Cpdb as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetDatafile | Returns an item of type Datafile as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetDirectory | Returns an item of type AjPDir which has been validated as a directory. |
ajAcdGetDirectoryName | Returns an item of type AjPStr which has been validated as a directory name |
ajAcdGetDirlist | Returns a list of files in a given directory. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetDiscretestates | Returns an item of type Discrete states as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetDiscretestatesSingle | Returns an from an array item of type Discrete states as defined in a named ACD item, which is an array of objects terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetDistances | Returns an item of type Distances as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetDistancesSingle | Returns an item of type Distances as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetFeatout | Returns an item of type FeatOut as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetFeatures | Returns an item of type Features as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetFeaturesall | Returns an input stream of an item of type Features as defined in a named ACD item. |
ajAcdGetFilelist | Returns a list of files given a comma-separated list. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetFloat | Returns an item of type Float as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetFloatDouble | Returns an item of type Float as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetFrequencies | Returns an item of type Frequencies as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetGraph | Returns a graph object which hold user graphics options. |
ajAcdGetGraphxy | Returns a graph object which hold user graphics options. |
ajAcdGetInfile | Returns an item of type file as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetInt | Returns an item of type ajint as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetIntLong | Returns an item of type ajlong as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetList | Returns an item of type List as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetListSingle | Returns a single item from an array of type List as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetMatrix | Returns an item of type Matrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetMatrixf | Returns an item of type Matrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetObo | Returns an item of type Obo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOboall | Returns an input stream of an item of type Obo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutassembly | Returns an item of type Outassembly as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutcodon | Returns an item of type Outcodon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutcpdb | Returns an item of type Outcpdb as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutdata | Returns an item of type Outdata as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutdir | Returns an item of type AjPDirout which has been validated as an output directory. |
ajAcdGetOutdirName | Returns an item of type AjPStr which has been validated as an output directory. |
ajAcdGetOutdiscrete | Returns an item of type Outdiscrete as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutdistance | Returns an item of type Outdistance as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutfile | Returns an item of type Outfile as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutfileName | Returns the filename of an item of type Outfile as defined in a named ACD item. The file is closed and can be reused. If the file had the append attribute set it still has the original contents. |
ajAcdGetOutfreq | Returns an item of type Outfreq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutmatrix | Returns an item of type Outmatrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutmatrixf | Returns an item of type Outmatrixf as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutobo | Returns an item of type Outobo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutproperties | Returns an item of type Outproperties as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutrefseq | Returns an item of type Outrefseq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutresource | Returns an item of type Outresource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutscop | Returns an item of type Outscop as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOuttaxon | Returns an item of type Outtaxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOuttext | Returns an item of type Outtext as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOuttree | Returns an item of type Outtree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOuturl | Returns an item of type Outurl as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutvariation | Returns an item of type Outvariation as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetOutxml | Returns an item of type Outxml as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetPattern | Returns an item of type Pattern as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetProperties | Returns an item of type Properties as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetRange | Returns an item of type Range as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetRefseq | Returns an item of type reference sequence as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetRegexp | Returns an item of type Regexp as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetRegexpSingle | Returns an item of type Regexp as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetReport | Returns an item of type Report as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetResource | Returns an item of type resource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetResourceall | Returns an input stream of an item of type Resource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetScop | Returns an item of type Scop as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSelect | Returns an item of type Select as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSelectSingle | Returns one item from an array of type Select as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeq | Returns an item of type Seq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeqall | Returns an item of type Seq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeqout | Returns an item of type Seqout as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeqoutall | Returns an item of type Seqoutall as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeqoutset | Returns an item of type Seqoutset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeqset | Returns an item of type Seqset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetSeqsetall | Returns an item of type Seqset array as defined in a named ACD item. The array is terminated by a NULL. |
ajAcdGetSeqsetallSingle | Returns an item of type Seqset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetString | Returns an item of type String as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetTaxon | Returns an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetTaxonall | Returns an input stream of an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetText | Returns an item of type Text as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetTextall | Returns an input stream of an item of type Text as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetToggle | Returns an item of type Toggle as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetTree | Returns an item of type Tree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetTreeSingle | Returns an item of type Tree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetUrl | Returns an item of type URL as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetUrlall | Returns an input stream of an item of type URL as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetValue | Returns the string value of any ACD item |
ajAcdGetValueDefault | Returns the default value of any ACD item |
ajAcdGetVariation | Returns an item of type variation loader as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetXml | Returns an item of type xml as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetXmlall | Returns an input stream of an item of type XML as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has. |
ajAcdGetpathC | Returns the full path of an application defined in an external: attribute within the application definition. If the application was defined by an EMBOSS_appname environment variable this will use the substitution made when the external attribute was validated. |
ajAcdGetpathS | Returns the full path of an application defined in an external: attribute within the application definition. If the application was defined by an EMBOSS_appname environment variable this will use the substitution made when the external attribute was validated. |
ajAcdIsUserdefinedC | Tests whether an ACD item has a value set by the user. |
ajAcdIsUserdefinedS | Tests whether an ACD item has a value set by the user. |
AjPAlign ajAcdGetAlign ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPAlign | RETURN | Alignment output object. Already opened by ajAlignOpent so this just returns the object |
From EMBOSS 2.1.0
AjPFloat ajAcdGetArray ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFloat | RETURN | Floating point array object |
From EMBOSS 1.0.0
AjPAssemload ajAcdGetAssembly ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPAssemload | RETURN | Assembly object |
From EMBOSS 6.5.0
AjBool ajAcdGetBoolean ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjBool | RETURN | Boolean value from ACD item |
From EMBOSS 6.0.0
AjPCod ajAcdGetCodon ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPCod | RETURN | Codon object. |
From EMBOSS 1.0.0
AjPFile ajAcdGetCpdb ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFile | RETURN | Cpdb input file. |
From EMBOSS 1.8.0
AjPFile ajAcdGetDatafile ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFile | RETURN | File object. The file was already opened by ajDatafileNewInNameS so this just returns the pointer. |
From EMBOSS 1.0.0
AjPDir ajAcdGetDirectory ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPDir | RETURN | Directory object |
From EMBOSS 1.0.0
AjPStr ajAcdGetDirectoryName ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr | RETURN | Directory path |
From EMBOSS 2.9.0
AjPList ajAcdGetDirlist ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPList | RETURN | List of files. |
From EMBOSS 1.9.0
AjPPhyloState* ajAcdGetDiscretestates ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloState* | RETURN | Discrete states object. The string was already set by acdSetDiscretestates so this just returns the pointer. |
From EMBOSS 2.8.0
AjPPhyloState ajAcdGetDiscretestatesSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloState | RETURN | Discrete states object. The data was already set by acdSetDiscretestates so this just returns the pointer. |
From EMBOSS 4.0.0
AjPPhyloDist* ajAcdGetDistances ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloDist* | RETURN | Distances object. The string was already set by acdSetDistances so this just returns the pointer. |
From EMBOSS 2.8.0
AjPPhyloDist ajAcdGetDistancesSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloDist | RETURN | Distances object. The string was already set by acdSetDistances so this just returns the pointer. |
From EMBOSS 5.0.0
AjPFeattabOut ajAcdGetFeatout ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFeattabOut | RETURN | Feature Table output object. Already opened by acdSetFeatout so this just returns the object |
From EMBOSS 1.0.0
AjPFeattable ajAcdGetFeatures ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFeattable | RETURN | Feature Table object. The table was already loaded by acdSetFeat so this just returns the pointer. |
From EMBOSS 6.0.0
AjPFeattaball ajAcdGetFeaturesall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFeattaball | RETURN | Features input stream |
From EMBOSS 6.4.0
AjPList ajAcdGetFilelist ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPList | RETURN | List of files. |
From EMBOSS 2.5.0
float ajAcdGetFloat ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
float | RETURN | Floating point value from ACD item |
From EMBOSS 1.0.0
double ajAcdGetFloatDouble ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
double | RETURN | Floating point value from ACD item |
From EMBOSS 6.1.0
AjPPhyloFreq ajAcdGetFrequencies ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloFreq | RETURN | Frequencies object. The string was already set by acdSetFrequencies so this just returns the pointer. |
From EMBOSS 2.8.0
AjPGraph ajAcdGetGraph ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPGraph | RETURN | Graph object. |
From EMBOSS 1.0.0
AjPGraph ajAcdGetGraphxy ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPGraph | RETURN | Graph object. |
From EMBOSS 1.0.0
AjPFile ajAcdGetInfile ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFile | RETURN | File object. The file was already opened by acdSetInfile so this just returns the pointer. |
From EMBOSS 1.0.0
ajint ajAcdGetInt ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
ajint | RETURN | Integer value from ACD item |
From EMBOSS 1.0.0
ajlong ajAcdGetIntLong ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
ajlong | RETURN | Integer value from ACD item |
From EMBOSS 6.1.0
AjPStr* ajAcdGetList ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr* | RETURN | String array of values with NULL for last element. |
From EMBOSS 1.0.0
AjPStr ajAcdGetListSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr | RETURN | String array of values with NULL for last element. |
From EMBOSS 4.0.0
AjPMatrix ajAcdGetMatrix ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPMatrix | RETURN | Matrix object. |
From EMBOSS 1.0.0
AjPMatrixf ajAcdGetMatrixf ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPMatrixf | RETURN | Float Matrix object. |
From EMBOSS 1.0.0
AjPObo ajAcdGetObo ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPObo | RETURN | Obo term object |
From EMBOSS 6.4.0
AjPOboall ajAcdGetOboall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOboall | RETURN | Obo input stream |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOutassembly ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.5.0
AjPOutfile ajAcdGetOutcodon ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutcpdb ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutdata ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPDirout ajAcdGetOutdir ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPDirout | RETURN | Output directory object |
From EMBOSS 2.9.0
AjPStr ajAcdGetOutdirName ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr | RETURN | String containing a directory name |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutdiscrete ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutdistance ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPFile ajAcdGetOutfile ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFile | RETURN | File object. The file was already opened by acdSetOutfile so this just returns the pointer. |
From EMBOSS 1.0.0
AjPStr ajAcdGetOutfileName ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr | RETURN | Filename. |
From EMBOSS 6.3.0
AjPOutfile ajAcdGetOutfreq ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutmatrix ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutmatrixf ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutobo ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOutproperties ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOutrefseq ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.5.0
AjPOutfile ajAcdGetOutresource ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOutscop ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOuttaxon ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOuttext ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOuttree ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 2.9.0
AjPOutfile ajAcdGetOuturl ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOutvariation ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.4.0
AjPOutfile ajAcdGetOutxml ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPOutfile | RETURN | File object. The file was already opened by acdSetOut so this just returns the pointer. |
From EMBOSS 6.6.0
AjPPatlistSeq ajAcdGetPattern ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPatlistSeq | RETURN | Compiled pattern list of sequence patterns. The original pattern string is available through a call to ajAcdGetValue |
From EMBOSS 4.0.0
AjPPhyloProp ajAcdGetProperties ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloProp | RETURN | Properties array. The data was already set by acdSetProperties so this just returns the pointer. |
From EMBOSS 2.8.0
AjPRange ajAcdGetRange ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPRange | RETURN | Range object. |
From EMBOSS 1.0.0
AjPRefseq ajAcdGetRefseq ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPRefseq | RETURN | Reference sequence object |
From EMBOSS 6.5.0
AjPPatlistRegex ajAcdGetRegexp ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPatlistRegex | RETURN | Compiled regular expression pattern. The original pattern string is available through a call to ajAcdGetValue |
From EMBOSS 1.0.0
AjPRegexp ajAcdGetRegexpSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPRegexp | RETURN | Compiled regular expression. The original pattern string is available through a call to ajAcdGetValue |
From EMBOSS 4.0.0
AjPReport ajAcdGetReport ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPReport | RETURN | Report output object. Already opened by ajReportOpen so this just returns the object |
From EMBOSS 2.0.0
AjPResource ajAcdGetResource ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPResource | RETURN | Data resource object |
From EMBOSS 6.4.0
AjPResourceall ajAcdGetResourceall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPResourceall | RETURN | Data resource input stream |
From EMBOSS 6.4.0
AjPFile ajAcdGetScop ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPFile | RETURN | Scop input file. |
From EMBOSS 1.8.0
AjPStr* ajAcdGetSelect ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr* | RETURN | String array of values with NULL as last element. |
From EMBOSS 1.0.0
AjPStr ajAcdGetSelectSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr | RETURN | String array of values with NULL as last element. |
From EMBOSS 4.0.0
AjPSeq ajAcdGetSeq ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeq | RETURN | Sequence object. The sequence was already loaded by acdSetSeq so this just returns the pointer. |
From EMBOSS 1.0.0
AjPSeqall ajAcdGetSeqall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqall | RETURN | Sequence stream object. The sequence was already loaded by acdSetSeqall so this just returns the pointer. |
From EMBOSS 1.0.0
AjPSeqout ajAcdGetSeqout ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqout | RETURN | Sequence output object. The file was already opened by acdSetSeqout so this just returns the pointer. |
From EMBOSS 1.0.0
AjPSeqout ajAcdGetSeqoutall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqout | RETURN | Sequence output object. The file was already opened by acdSetSeqoutall so this just returns the pointer. |
From EMBOSS 1.0.0
AjPSeqout ajAcdGetSeqoutset ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqout | RETURN | Sequence output object. The file was already opened by acdSetSeqoutset so this just returns the pointer. |
From EMBOSS 1.0.0
AjPSeqset ajAcdGetSeqset ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqset | RETURN | Sequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer. |
From EMBOSS 1.0.0
AjPSeqset* ajAcdGetSeqsetall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqset* | RETURN | Sequence setall object. The sequence was already loaded by acdSetSeqset so this just returns the pointer. |
From EMBOSS 2.8.0
AjPSeqset ajAcdGetSeqsetallSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPSeqset | RETURN | Sequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer. |
From EMBOSS 4.0.0
AjPStr ajAcdGetString ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPStr | RETURN | String object. The string was already set by acdSetString so this just returns the pointer. |
From EMBOSS 1.0.0
AjPTax ajAcdGetTaxon ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPTax | RETURN | Taxon object |
From EMBOSS 6.4.0
AjPTaxall ajAcdGetTaxonall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPTaxall | RETURN | Taxon input stream |
From EMBOSS 6.4.0
AjPText ajAcdGetText ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPText | RETURN | Text object |
From EMBOSS 6.4.0
AjPTextall ajAcdGetTextall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPTextall | RETURN | Text input stream |
From EMBOSS 6.4.0
AjBool ajAcdGetToggle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjBool | RETURN | Boolean value from ACD item |
From EMBOSS 2.9.0
AjPPhyloTree* ajAcdGetTree ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloTree* | RETURN | Tree object. The data was already set by acdSetTree so this just returns the pointer. |
From EMBOSS 2.8.0
AjPPhyloTree ajAcdGetTreeSingle ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPPhyloTree | RETURN | Tree object. The data was already set by acdSetTree so this just returns the pointer. |
From EMBOSS 4.0.0
AjPUrl ajAcdGetUrl ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPUrl | RETURN | URL object |
From EMBOSS 6.4.0
AjPUrlall ajAcdGetUrlall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPUrlall | RETURN | URL input stream |
From EMBOSS 6.4.0
const AjPStr ajAcdGetValue ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
const AjPStr | RETURN | String object. The string was already set by acdSetString so this just returns the pointer. |
From EMBOSS 4.0.0
const AjPStr ajAcdGetValueDefault ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
const AjPStr | RETURN | Default value. |
From EMBOSS 6.0.0
AjPVarload ajAcdGetVariation ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPVarload | RETURN | Variation loader object |
From EMBOSS 6.4.0
AjPXml ajAcdGetXml ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPXml | RETURN | Xml object |
From EMBOSS 6.6.0
AjPXmlall ajAcdGetXmlall ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjPXmlall | RETURN | URL input stream |
From EMBOSS 6.6.0
const AjPStr ajAcdGetpathC ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | External application name |
const AjPStr | RETURN | Executable application name |
From EMBOSS 6.2.0
const AjPStr ajAcdGetpathS ( const AjPStr strtoken );
Type | Name | Read/Write | Description |
---|---|---|---|
const AjPStr | strtoken | Input | External application name |
const AjPStr | RETURN | Executable application name |
From EMBOSS 6.2.0
AjBool ajAcdIsUserdefinedC ( const char* token );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | token | Input | Text token name |
AjBool | RETURN | True if token is not found as an ACD object name |
From EMBOSS 6.2.0
AjBool ajAcdIsUserdefinedS ( const AjPStr strtoken );
Type | Name | Read/Write | Description |
---|---|---|---|
const AjPStr | strtoken | Input | Text token name |
AjBool | RETURN | True if token is not found as an ACD object name |
From EMBOSS 6.2.0
Functions:
ajAcdSetControl | Sets special qualifiers which were originally provided via the command line. |
AjBool ajAcdSetControl ( const char* optionName );
Type | Name | Read/Write | Description |
---|---|---|---|
const char* | optionName | Input | option name |
AjBool | RETURN | ajTrue if option was recognised |
From EMBOSS 2.7.0
Functions:
ajAcdPrintAppl | Report details of all known ACD attributes for all applications. For use by EMBOSS entrails. |
ajAcdPrintQual | Report details of all known ACD qualifiers for all applications. For use by EMBOSS entrails. |
ajAcdPrintType | Report details of all known ACD types. For use by EMBOSS entrails. |
void ajAcdPrintAppl ( AjPFile outf, AjBool full );
Type | Name | Read/Write | Description |
---|---|---|---|
AjPFile | outf | Modify | Output file |
AjBool | full | Input | Full report - currently no extra details printed |
void | RETURN |
From EMBOSS 4.0.0
void ajAcdPrintQual ( AjPFile outf, AjBool full );
Type | Name | Read/Write | Description |
---|---|---|---|
AjPFile | outf | Modify | Output file |
AjBool | full | Input | Full report - currently no extra details printed |
void | RETURN |
From EMBOSS 2.8.0
void ajAcdPrintType ( AjPFile outf, AjBool full );
Type | Name | Read/Write | Description |
---|---|---|---|
AjPFile | outf | Modify | Output file |
AjBool | full | Input | Full report |
void | RETURN |
From EMBOSS 1.0.0
Functions:
ajAcdExit | Reports any unused ACD values |
void ajAcdExit ( AjBool silent );
Type | Name | Read/Write | Description |
---|---|---|---|
AjBool | silent | Input | Turn off messages (used when some messages are expected but can be ignored). |
void | RETURN |
From EMBOSS 2.4.0
Functions:
ajAcdUnused | Dummy function to catch all unused functions defined in the ajacd source file. |
void ajAcdUnused ( void );
Type | Name | Read/Write | Description |
---|---|---|---|
void | RETURN |
From EMBOSS 4.0.0
Functions:
ajAcdedamParse | Parse an EDAM term from a relations attribute |
ajAcdtypeGetGroup | Return the ACD group for an ACD datatype |
AjBool ajAcdedamParse ( const AjPStr relation, AjPStr* id, AjPStr* namespace, AjPStr* name );
Type | Name | Read/Write | Description |
---|---|---|---|
const AjPStr | relation | Input | Relation single attribute value |
AjPStr* | id | Output | EDAM term numeric id |
AjPStr* | namespace | Output | EDAM term namespace |
AjPStr* | name | Output | EDAM term name |
AjBool | RETURN | True on success |
From EMBOSS 6.4.0
const char* ajAcdtypeGetGroup ( const AjPStr type );
Type | Name | Read/Write | Description |
---|---|---|---|
const AjPStr | type | Input | ACD type name |
const char* | RETURN | Group name |
From EMBOSS 6.4.0