ajacd.c

Datatypes:
none ACD internals


Datatype: none

Function is for processing ACD internals.

Sections:
initialisationMiscellaneous
returnMiscellaneous
internalsMiscellaneous
printMiscellaneous
exitMiscellaneous
unusedMiscellaneous
edamMiscellaneous


Section: initialisation

Initialises everything needed for ACD processing.

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


Function ajAcdInit

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.

Prototype

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

TypeNameRead/WriteDescription
const char*pgmInputApplication name, used as the name of the ACD file
ajintargcInputNumber of arguments provided on the command line, usually passed as-is by the calling application.
char* const[]argvInputActual arguments as an array of text.
void RETURN

From EMBOSS 1.0.0


Function 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.

Prototype

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

TypeNameRead/WriteDescription
const char*pgmInputApplication name, used as the name of the ACD file
ajintargcInputNumber of arguments provided on the command line, usually passed as-is by the calling application.
char* const[]argvInputActual arguments as an array of text.
const char*packageInputPackage name, used to find the ACD file
const char*packversionInputPackage version
void RETURN

From EMBOSS 6.2.0


Section: return

Returns values to the calling program.

Functions:
ajAcdGetAlignReturns 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.
ajAcdGetArrayReturns 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.
ajAcdGetAssemblyReturns 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.
ajAcdGetBooleanReturns 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.
ajAcdGetCodonReturns 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.
ajAcdGetCpdbReturns 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.
ajAcdGetDatafileReturns 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.
ajAcdGetDirectoryReturns an item of type AjPDir which has been validated as a directory.
ajAcdGetDirectoryNameReturns an item of type AjPStr which has been validated as a directory name
ajAcdGetDirlistReturns 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.
ajAcdGetDiscretestatesReturns 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.
ajAcdGetDiscretestatesSingleReturns 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.
ajAcdGetDistancesReturns 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.
ajAcdGetDistancesSingleReturns 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.
ajAcdGetFeatoutReturns 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.
ajAcdGetFeaturesReturns 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.
ajAcdGetFeaturesallReturns an input stream of an item of type Features as defined in a named ACD item.
ajAcdGetFilelistReturns 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.
ajAcdGetFloatReturns 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.
ajAcdGetFloatDoubleReturns 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.
ajAcdGetFrequenciesReturns 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.
ajAcdGetGraphReturns a graph object which hold user graphics options.
ajAcdGetGraphxyReturns a graph object which hold user graphics options.
ajAcdGetInfileReturns 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.
ajAcdGetIntReturns 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.
ajAcdGetIntLongReturns 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.
ajAcdGetListReturns 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.
ajAcdGetListSingleReturns 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.
ajAcdGetMatrixReturns 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.
ajAcdGetMatrixfReturns 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.
ajAcdGetOboReturns 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.
ajAcdGetOboallReturns 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.
ajAcdGetOutassemblyReturns 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.
ajAcdGetOutcodonReturns 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.
ajAcdGetOutcpdbReturns 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.
ajAcdGetOutdataReturns 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.
ajAcdGetOutdirReturns an item of type AjPDirout which has been validated as an output directory.
ajAcdGetOutdirNameReturns an item of type AjPStr which has been validated as an output directory.
ajAcdGetOutdiscreteReturns 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.
ajAcdGetOutdistanceReturns 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.
ajAcdGetOutfileReturns 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.
ajAcdGetOutfileNameReturns 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.
ajAcdGetOutfreqReturns 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.
ajAcdGetOutmatrixReturns 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.
ajAcdGetOutmatrixfReturns 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.
ajAcdGetOutoboReturns 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.
ajAcdGetOutpropertiesReturns 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.
ajAcdGetOutrefseqReturns 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.
ajAcdGetOutresourceReturns 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.
ajAcdGetOutscopReturns 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.
ajAcdGetOuttaxonReturns 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.
ajAcdGetOuttextReturns 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.
ajAcdGetOuttreeReturns 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.
ajAcdGetOuturlReturns 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.
ajAcdGetOutvariationReturns 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.
ajAcdGetOutxmlReturns 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.
ajAcdGetPatternReturns 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.
ajAcdGetPropertiesReturns 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.
ajAcdGetRangeReturns 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.
ajAcdGetRefseqReturns 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.
ajAcdGetRegexpReturns 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.
ajAcdGetRegexpSingleReturns 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.
ajAcdGetReportReturns 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.
ajAcdGetResourceReturns 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.
ajAcdGetResourceallReturns 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.
ajAcdGetScopReturns 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.
ajAcdGetSelectReturns 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.
ajAcdGetSelectSingleReturns 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.
ajAcdGetSeqReturns 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.
ajAcdGetSeqallReturns 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.
ajAcdGetSeqoutReturns 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.
ajAcdGetSeqoutallReturns 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.
ajAcdGetSeqoutsetReturns 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.
ajAcdGetSeqsetReturns 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.
ajAcdGetSeqsetallReturns an item of type Seqset array as defined in a named ACD item. The array is terminated by a NULL.
ajAcdGetSeqsetallSingleReturns 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.
ajAcdGetStringReturns 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.
ajAcdGetTaxonReturns 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.
ajAcdGetTaxonallReturns 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.
ajAcdGetTextReturns 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.
ajAcdGetTextallReturns 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.
ajAcdGetToggleReturns 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.
ajAcdGetTreeReturns 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.
ajAcdGetTreeSingleReturns 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.
ajAcdGetUrlReturns 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.
ajAcdGetUrlallReturns 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.
ajAcdGetValueReturns the string value of any ACD item
ajAcdGetValueDefaultReturns the default value of any ACD item
ajAcdGetVariationReturns 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.
ajAcdGetXmlReturns 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.
ajAcdGetXmlallReturns 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.
ajAcdGetpathCReturns 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.
ajAcdGetpathSReturns 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.
ajAcdIsUserdefinedCTests whether an ACD item has a value set by the user.
ajAcdIsUserdefinedSTests whether an ACD item has a value set by the user.


Function ajAcdGetAlign

Returns an item of type Align as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPAlign ajAcdGetAlign (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPAlign RETURNAlignment output object. Already opened by ajAlignOpent so this just returns the object

From EMBOSS 2.1.0


Function ajAcdGetArray

Returns an item of type array as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFloat ajAcdGetArray (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFloat RETURNFloating point array object

From EMBOSS 1.0.0


Function 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.

Prototype

AjPAssemload ajAcdGetAssembly (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPAssemload RETURNAssembly object

From EMBOSS 6.5.0


Function ajAcdGetBoolean

Returns an item of type Bool as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjBool ajAcdGetBoolean (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjBool RETURNBoolean value from ACD item

From EMBOSS 6.0.0


Function ajAcdGetCodon

Returns an item of type Codon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPCod ajAcdGetCodon (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPCod RETURNCodon object.

From EMBOSS 1.0.0


Function ajAcdGetCpdb

Returns an item of type Cpdb as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFile ajAcdGetCpdb (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFile RETURNCpdb input file.

From EMBOSS 1.8.0


Function ajAcdGetDatafile

Returns an item of type Datafile as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFile ajAcdGetDatafile (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFile RETURNFile object. The file was already opened by ajDatafileNewInNameS so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetDirectory

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

Prototype

AjPDir ajAcdGetDirectory (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPDir RETURNDirectory object

From EMBOSS 1.0.0


Function ajAcdGetDirectoryName

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

Prototype

AjPStr ajAcdGetDirectoryName (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr RETURNDirectory path

From EMBOSS 2.9.0


Function ajAcdGetDirlist

Returns a list of files in a given directory. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPList ajAcdGetDirlist (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPList RETURNList of files.

From EMBOSS 1.9.0


Function ajAcdGetDiscretestates

Returns an item of type Discrete states as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloState* ajAcdGetDiscretestates (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloState* RETURNDiscrete states object. The string was already set by acdSetDiscretestates so this just returns the pointer.

From EMBOSS 2.8.0


Function ajAcdGetDiscretestatesSingle

Returns an from an array item of type Discrete states as defined in a named ACD item, which is an array of objects terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloState ajAcdGetDiscretestatesSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloState RETURNDiscrete states object. The data was already set by acdSetDiscretestates so this just returns the pointer.

From EMBOSS 4.0.0


Function ajAcdGetDistances

Returns an item of type Distances as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloDist* ajAcdGetDistances (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloDist* RETURNDistances object. The string was already set by acdSetDistances so this just returns the pointer.

From EMBOSS 2.8.0


Function ajAcdGetDistancesSingle

Returns an item of type Distances as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloDist ajAcdGetDistancesSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloDist RETURNDistances object. The string was already set by acdSetDistances so this just returns the pointer.

From EMBOSS 5.0.0


Function ajAcdGetFeatout

Returns an item of type FeatOut as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFeattabOut ajAcdGetFeatout (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFeattabOut RETURNFeature Table output object. Already opened by acdSetFeatout so this just returns the object

From EMBOSS 1.0.0


Function ajAcdGetFeatures

Returns an item of type Features as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFeattable ajAcdGetFeatures (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFeattable RETURNFeature Table object. The table was already loaded by acdSetFeat so this just returns the pointer.

From EMBOSS 6.0.0


Function ajAcdGetFeaturesall

Returns an input stream of an item of type Features as defined in a named ACD item.

Prototype

AjPFeattaball ajAcdGetFeaturesall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFeattaball RETURNFeatures input stream

From EMBOSS 6.4.0


Function ajAcdGetFilelist

Returns a list of files given a comma-separated list. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPList ajAcdGetFilelist (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPList RETURNList of files.

From EMBOSS 2.5.0


Function ajAcdGetFloat

Returns an item of type Float as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

float ajAcdGetFloat (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
float RETURNFloating point value from ACD item

From EMBOSS 1.0.0


Function ajAcdGetFloatDouble

Returns an item of type Float as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

double ajAcdGetFloatDouble (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
double RETURNFloating point value from ACD item

From EMBOSS 6.1.0


Function ajAcdGetFrequencies

Returns an item of type Frequencies as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloFreq ajAcdGetFrequencies (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloFreq RETURNFrequencies object. The string was already set by acdSetFrequencies so this just returns the pointer.

From EMBOSS 2.8.0


Function ajAcdGetGraph

Returns a graph object which hold user graphics options.

Prototype

AjPGraph ajAcdGetGraph (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPGraph RETURNGraph object.

From EMBOSS 1.0.0


Function ajAcdGetGraphxy

Returns a graph object which hold user graphics options.

Prototype

AjPGraph ajAcdGetGraphxy (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPGraph RETURNGraph object.

From EMBOSS 1.0.0


Function ajAcdGetInfile

Returns an item of type file as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFile ajAcdGetInfile (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFile RETURNFile object. The file was already opened by acdSetInfile so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetInt

Returns an item of type ajint as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

ajint ajAcdGetInt (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
ajint RETURNInteger value from ACD item

From EMBOSS 1.0.0


Function ajAcdGetIntLong

Returns an item of type ajlong as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

ajlong ajAcdGetIntLong (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
ajlong RETURNInteger value from ACD item

From EMBOSS 6.1.0


Function ajAcdGetList

Returns an item of type List as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPStr* ajAcdGetList (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr* RETURNString array of values with NULL for last element.

From EMBOSS 1.0.0


Function ajAcdGetListSingle

Returns a single item from an array of type List as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPStr ajAcdGetListSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr RETURNString array of values with NULL for last element.

From EMBOSS 4.0.0


Function ajAcdGetMatrix

Returns an item of type Matrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPMatrix ajAcdGetMatrix (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPMatrix RETURNMatrix object.

From EMBOSS 1.0.0


Function ajAcdGetMatrixf

Returns an item of type Matrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPMatrixf ajAcdGetMatrixf (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPMatrixf RETURNFloat Matrix object.

From EMBOSS 1.0.0


Function ajAcdGetObo

Returns an item of type Obo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPObo ajAcdGetObo (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPObo RETURNObo term object

From EMBOSS 6.4.0


Function ajAcdGetOboall

Returns an input stream of an item of type Obo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOboall ajAcdGetOboall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOboall RETURNObo input stream

From EMBOSS 6.4.0


Function 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.

Prototype

AjPOutfile ajAcdGetOutassembly (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.5.0


Function ajAcdGetOutcodon

Returns an item of type Outcodon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutcodon (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutcpdb

Returns an item of type Outcpdb as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutcpdb (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutdata

Returns an item of type Outdata as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutdata (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutdir

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

Prototype

AjPDirout ajAcdGetOutdir (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPDirout RETURNOutput directory object

From EMBOSS 2.9.0


Function ajAcdGetOutdirName

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

Prototype

AjPStr ajAcdGetOutdirName (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr RETURNString containing a directory name

From EMBOSS 2.9.0


Function ajAcdGetOutdiscrete

Returns an item of type Outdiscrete as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutdiscrete (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutdistance

Returns an item of type Outdistance as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutdistance (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutfile

Returns an item of type Outfile as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFile ajAcdGetOutfile (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFile RETURNFile object. The file was already opened by acdSetOutfile so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetOutfileName

Returns the filename of an item of type Outfile as defined in a named ACD item. The file is closed and can be reused. If the file had the append attribute set it still has the original contents.

Prototype

AjPStr ajAcdGetOutfileName (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr RETURNFilename.

From EMBOSS 6.3.0


Function ajAcdGetOutfreq

Returns an item of type Outfreq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutfreq (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutmatrix

Returns an item of type Outmatrix as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutmatrix (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutmatrixf

Returns an item of type Outmatrixf as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutmatrixf (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOutobo

Returns an item of type Outobo as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutobo (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0


Function ajAcdGetOutproperties

Returns an item of type Outproperties as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutproperties (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function 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.

Prototype

AjPOutfile ajAcdGetOutrefseq (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.5.0


Function ajAcdGetOutresource

Returns an item of type Outresource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutresource (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0


Function ajAcdGetOutscop

Returns an item of type Outscop as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutscop (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOuttaxon

Returns an item of type Outtaxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOuttaxon (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0


Function ajAcdGetOuttext

Returns an item of type Outtext as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOuttext (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0


Function ajAcdGetOuttree

Returns an item of type Outtree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOuttree (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 2.9.0


Function ajAcdGetOuturl

Returns an item of type Outurl as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOuturl (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0


Function ajAcdGetOutvariation

Returns an item of type Outvariation as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPOutfile ajAcdGetOutvariation (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.4.0


Function 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.

Prototype

AjPOutfile ajAcdGetOutxml (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPOutfile RETURNFile object. The file was already opened by acdSetOut so this just returns the pointer.

From EMBOSS 6.6.0


Function ajAcdGetPattern

Returns an item of type Pattern as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPatlistSeq ajAcdGetPattern (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPatlistSeq RETURNCompiled pattern list of sequence patterns. The original pattern string is available through a call to ajAcdGetValue

From EMBOSS 4.0.0


Function ajAcdGetProperties

Returns an item of type Properties as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloProp ajAcdGetProperties (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloProp RETURNProperties array. The data was already set by acdSetProperties so this just returns the pointer.

From EMBOSS 2.8.0


Function ajAcdGetRange

Returns an item of type Range as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPRange ajAcdGetRange (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPRange RETURNRange object.

From EMBOSS 1.0.0


Function 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.

Prototype

AjPRefseq ajAcdGetRefseq (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPRefseq RETURNReference sequence object

From EMBOSS 6.5.0


Function ajAcdGetRegexp

Returns an item of type Regexp as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPatlistRegex ajAcdGetRegexp (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPatlistRegex RETURNCompiled regular expression pattern. The original pattern string is available through a call to ajAcdGetValue

From EMBOSS 1.0.0


Function ajAcdGetRegexpSingle

Returns an item of type Regexp as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPRegexp ajAcdGetRegexpSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPRegexp RETURNCompiled regular expression. The original pattern string is available through a call to ajAcdGetValue

From EMBOSS 4.0.0


Function ajAcdGetReport

Returns an item of type Report as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPReport ajAcdGetReport (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPReport RETURNReport output object. Already opened by ajReportOpen so this just returns the object

From EMBOSS 2.0.0


Function ajAcdGetResource

Returns an item of type resource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPResource ajAcdGetResource (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPResource RETURNData resource object

From EMBOSS 6.4.0


Function ajAcdGetResourceall

Returns an input stream of an item of type Resource as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPResourceall ajAcdGetResourceall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPResourceall RETURNData resource input stream

From EMBOSS 6.4.0


Function ajAcdGetScop

Returns an item of type Scop as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPFile ajAcdGetScop (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPFile RETURNScop input file.

From EMBOSS 1.8.0


Function ajAcdGetSelect

Returns an item of type Select as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPStr* ajAcdGetSelect (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr* RETURNString array of values with NULL as last element.

From EMBOSS 1.0.0


Function ajAcdGetSelectSingle

Returns one item from an array of type Select as defined in a named ACD item, which is an array of strings terminated by a null value. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPStr ajAcdGetSelectSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr RETURNString array of values with NULL as last element.

From EMBOSS 4.0.0


Function ajAcdGetSeq

Returns an item of type Seq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeq ajAcdGetSeq (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeq RETURNSequence object. The sequence was already loaded by acdSetSeq so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetSeqall

Returns an item of type Seq as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeqall ajAcdGetSeqall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqall RETURNSequence stream object. The sequence was already loaded by acdSetSeqall so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetSeqout

Returns an item of type Seqout as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeqout ajAcdGetSeqout (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqout RETURNSequence output object. The file was already opened by acdSetSeqout so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetSeqoutall

Returns an item of type Seqoutall as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeqout ajAcdGetSeqoutall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqout RETURNSequence output object. The file was already opened by acdSetSeqoutall so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetSeqoutset

Returns an item of type Seqoutset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeqout ajAcdGetSeqoutset (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqout RETURNSequence output object. The file was already opened by acdSetSeqoutset so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetSeqset

Returns an item of type Seqset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeqset ajAcdGetSeqset (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqset RETURNSequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetSeqsetall

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

Prototype

AjPSeqset* ajAcdGetSeqsetall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqset* RETURNSequence setall object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

From EMBOSS 2.8.0


Function ajAcdGetSeqsetallSingle

Returns an item of type Seqset as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPSeqset ajAcdGetSeqsetallSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPSeqset RETURNSequence set object. The sequence was already loaded by acdSetSeqset so this just returns the pointer.

From EMBOSS 4.0.0


Function ajAcdGetString

Returns an item of type String as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPStr ajAcdGetString (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPStr RETURNString object. The string was already set by acdSetString so this just returns the pointer.

From EMBOSS 1.0.0


Function ajAcdGetTaxon

Returns an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPTax ajAcdGetTaxon (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPTax RETURNTaxon object

From EMBOSS 6.4.0


Function ajAcdGetTaxonall

Returns an input stream of an item of type Taxon as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPTaxall ajAcdGetTaxonall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPTaxall RETURNTaxon input stream

From EMBOSS 6.4.0


Function ajAcdGetText

Returns an item of type Text as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPText ajAcdGetText (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPText RETURNText object

From EMBOSS 6.4.0


Function ajAcdGetTextall

Returns an input stream of an item of type Text as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPTextall ajAcdGetTextall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPTextall RETURNText input stream

From EMBOSS 6.4.0


Function ajAcdGetToggle

Returns an item of type Toggle as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjBool ajAcdGetToggle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjBool RETURNBoolean value from ACD item

From EMBOSS 2.9.0


Function ajAcdGetTree

Returns an item of type Tree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloTree* ajAcdGetTree (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloTree* RETURNTree object. The data was already set by acdSetTree so this just returns the pointer.

From EMBOSS 2.8.0


Function ajAcdGetTreeSingle

Returns an item of type Tree as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPPhyloTree ajAcdGetTreeSingle (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPPhyloTree RETURNTree object. The data was already set by acdSetTree so this just returns the pointer.

From EMBOSS 4.0.0


Function ajAcdGetUrl

Returns an item of type URL as defined in a named ACD item. Called by the application after all ACD values have been set, and simply returns what the ACD item already has.

Prototype

AjPUrl ajAcdGetUrl (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPUrl RETURNURL object

From EMBOSS 6.4.0


Function 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.

Prototype

AjPUrlall ajAcdGetUrlall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPUrlall RETURNURL input stream

From EMBOSS 6.4.0


Function ajAcdGetValue

Returns the string value of any ACD item

Prototype

const AjPStr ajAcdGetValue (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
const AjPStr RETURNString object. The string was already set by acdSetString so this just returns the pointer.

From EMBOSS 4.0.0


Function ajAcdGetValueDefault

Returns the default value of any ACD item

Prototype

const AjPStr ajAcdGetValueDefault (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
const AjPStr RETURNDefault value.

From EMBOSS 6.0.0


Function 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.

Prototype

AjPVarload ajAcdGetVariation (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPVarload RETURNVariation loader object

From EMBOSS 6.4.0


Function 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.

Prototype

AjPXml ajAcdGetXml (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPXml RETURNXml object

From EMBOSS 6.6.0


Function 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.

Prototype

AjPXmlall ajAcdGetXmlall (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjPXmlall RETURNURL input stream

From EMBOSS 6.6.0


Function ajAcdGetpathC

Returns the full path of an application defined in an external: attribute within the application definition. If the application was defined by an EMBOSS_appname environment variable this will use the substitution made when the external attribute was validated.

Prototype

const AjPStr ajAcdGetpathC (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputExternal application name
const AjPStr RETURNExecutable application name

From EMBOSS 6.2.0


Function 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.

Prototype

const AjPStr ajAcdGetpathS (
      const AjPStr strtoken
);

TypeNameRead/WriteDescription
const AjPStrstrtokenInputExternal application name
const AjPStr RETURNExecutable application name

From EMBOSS 6.2.0


Function ajAcdIsUserdefinedC

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

Prototype

AjBool ajAcdIsUserdefinedC (
      const char* token
);

TypeNameRead/WriteDescription
const char*tokenInputText token name
AjBool RETURNTrue if token is not found as an ACD object name

From EMBOSS 6.2.0


Function ajAcdIsUserdefinedS

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

Prototype

AjBool ajAcdIsUserdefinedS (
      const AjPStr strtoken
);

TypeNameRead/WriteDescription
const AjPStrstrtokenInputText token name
AjBool RETURNTrue if token is not found as an ACD object name

From EMBOSS 6.2.0


Section: internals

Sets internal values

Functions:
ajAcdSetControlSets special qualifiers which were originally provided via the command line.


Function ajAcdSetControl

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

Prototype

AjBool ajAcdSetControl (
      const char* optionName
);

TypeNameRead/WriteDescription
const char*optionNameInputoption name
AjBool RETURNajTrue if option was recognised

From EMBOSS 2.7.0


Section: print

Functions:
ajAcdPrintApplReport details of all known ACD attributes for all applications. For use by EMBOSS entrails.
ajAcdPrintQualReport details of all known ACD qualifiers for all applications. For use by EMBOSS entrails.
ajAcdPrintTypeReport details of all known ACD types. For use by EMBOSS entrails.


Function ajAcdPrintAppl

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

Prototype

void ajAcdPrintAppl (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull report - currently no extra details printed
void RETURN

From EMBOSS 4.0.0


Function ajAcdPrintQual

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

Prototype

void ajAcdPrintQual (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull report - currently no extra details printed
void RETURN

From EMBOSS 2.8.0


Function ajAcdPrintType

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

Prototype

void ajAcdPrintType (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull report
void RETURN

From EMBOSS 1.0.0


Section: exit

Functions called on exit

Functions:
ajAcdExitReports any unused ACD values


Function ajAcdExit

Reports any unused ACD values

Prototype

void ajAcdExit (
      AjBool silent
);

TypeNameRead/WriteDescription
AjBoolsilentInputTurn off messages (used when some messages are expected but can be ignored).
void RETURN

From EMBOSS 2.4.0


Section: unused

Functions:
ajAcdUnusedDummy function to catch all unused functions defined in the ajacd source file.


Function ajAcdUnused

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

Prototype

void ajAcdUnused (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 4.0.0


Section: edam

Functions:
ajAcdedamParseParse an EDAM term from a relations attribute
ajAcdtypeGetGroupReturn the ACD group for an ACD datatype


Function ajAcdedamParse

Parse an EDAM term from a relations attribute

Prototype

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

TypeNameRead/WriteDescription
const AjPStrrelationInputRelation single attribute value
AjPStr*idOutputEDAM term numeric id
AjPStr*namespaceOutputEDAM term namespace
AjPStr*nameOutputEDAM term name
AjBool RETURNTrue on success

From EMBOSS 6.4.0


Function ajAcdtypeGetGroup

Return the ACD group for an ACD datatype

Prototype

const char* ajAcdtypeGetGroup (
      const AjPStr type
);

TypeNameRead/WriteDescription
const AjPStrtypeInputACD type name
const char* RETURNGroup name

From EMBOSS 6.4.0