embgroup.c

Function embGrpGetProgGroups

Optionally constructs a path to the directory of normal EMBOSS or embassy ACD files. Calls grpGetAcdFiles to construct lists of the group, doc and program name information.

Prototype

void embGrpGetProgGroups (
      AjPList glist,
      AjPList alpha,
      char* const[] env,
      AjBool emboss,
      AjBool embassy,
      const AjPStr embassyname,
      AjBool explode,
      AjBool colon,
      AjBool gui
);

Type Name Read/Write Description

AjPList glist Output List of groups of programs

AjPList alpha Output Alphabetic list of programs

char* const[] env Input Environment passed in from C main() parameters

AjBool emboss Input Read in EMBOSS ACD data

AjBool embassy Input Read in EMBASSY ACD data

const AjPStr embassyname Input Name of embassy package. default is to search for all

AjBool explode Input Expand group names around ':'

AjBool colon Input Retain ':' in group names

AjBool gui Input Only report programs that are OK in GUIs

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`glist`	Output	List of groups of programs
`AjPList`	`alpha`	Output	Alphabetic list of programs
`char* const[]`	`env`	Input	Environment passed in from C main() parameters
`AjBool`	`emboss`	Input	Read in EMBOSS ACD data
`AjBool`	`embassy`	Input	Read in EMBASSY ACD data
`const AjPStr`	`embassyname`	Input	Name of embassy package. default is to search for all
`AjBool`	`explode`	Input	Expand group names around ':'
`AjBool`	`colon`	Input	Retain ':' in group names
`AjBool`	`gui`	Input	Only report programs that are OK in GUIs
`void`		RETURN

From EMBOSS 1.0.0

Function embGrpGetEmbassy

Optionally constructs a path to the directory of normal EMBOSS or embassy ACD files. Calls grpGetAcdFiles to construct lists of the group, doc and program name information.

Prototype

AjBool embGrpGetEmbassy (
      const AjPStr appname,
      AjPStr* embassyname
);

Type Name Read/Write Description

const AjPStr appname Input Application name

AjPStr* embassyname Output Embassy package attribute value, or an empty string if in the main package

AjBool RETURN ajTrue if an ACD file was found

Type	Name	Read/Write	Description
`const AjPStr`	`appname`	Input	Application name
`AjPStr*`	`embassyname`	Output	Embassy package attribute value, or an empty string if in the main package
`AjBool`		RETURN	ajTrue if an ACD file was found

From EMBOSS 4.1.0

Function embGrpMakeNewGnode

Creates a new pointer to a Gnode struct for holding a group's name and pointer to a list of programs (also held in Gnodes).

Prototype

EmbPGroupTop embGrpMakeNewGnode (
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr name Input Name of the group

EmbPGroupTop RETURN pointer to a new GPnode struct

Type	Name	Read/Write	Description
`const AjPStr`	`name`	Input	Name of the group
`EmbPGroupTop`		RETURN	pointer to a new GPnode struct

From EMBOSS 2.0.0

Function embGrpMakeNewPnode

Creates a new pointer to a Gnode struct for holding a program's name and documentation.

Prototype

EmbPGroupProg embGrpMakeNewPnode (
      const AjPStr name,
      const AjPStr doc,
      const AjPStr keywords,
      const AjPStr package
);

Type Name Read/Write Description

const AjPStr name Input Name of the program

const AjPStr doc Input Description of the program

const AjPStr keywords Input Keywords for this program with underscores for spaces and with spaces as separators

const AjPStr package Input Name of the package

EmbPGroupProg RETURN pointer to a new gnode struct

Type	Name	Read/Write	Description
`const AjPStr`	`name`	Input	Name of the program
`const AjPStr`	`doc`	Input	Description of the program
`const AjPStr`	`keywords`	Input	Keywords for this program with underscores for spaces and with spaces as separators
`const AjPStr`	`package`	Input	Name of the package
`EmbPGroupProg`		RETURN	pointer to a new gnode struct

From EMBOSS 2.0.0

Function embGrpSortGroupsList

Sort a list of GPnodes by their name.

Prototype

void embGrpSortGroupsList (
      AjPList groupslist
);

Type Name Read/Write Description

AjPList groupslist Modify List to sort

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`groupslist`	Modify	List to sort
`void`		RETURN

From EMBOSS 2.0.0

Function embGrpSortProgsList

Sort a list of Pnodes by their name.

Prototype

void embGrpSortProgsList (
      AjPList progslist
);

Type Name Read/Write Description

AjPList progslist Modify List to sort

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`progslist`	Modify	List to sort
`void`		RETURN

From EMBOSS 4.0.0

Function embGrpCompareTwoGnodes

Compare two Gnodes as case-insensitive strings.

Prototype

ajint embGrpCompareTwoGnodes (
      const void* a,
      const void* b
);

Type Name Read/Write Description

const void* a Input First node

const void* b Input Second node

ajint RETURN Compare value (-1, 0, +1)

Type	Name	Read/Write	Description
`const void*`	`a`	Input	First node
`const void*`	`b`	Input	Second node
`ajint`		RETURN	Compare value (-1, 0, +1)

From EMBOSS 2.0.0

Function embGrpCompareTwoPnodes

Compare two Pnodes as case-insensitive strings.

Prototype

ajint embGrpCompareTwoPnodes (
      const void* a,
      const void* b
);

Type Name Read/Write Description

const void* a Input First node

const void* b Input Second node

ajint RETURN Compare value (-1, 0, +1)

Type	Name	Read/Write	Description
`const void*`	`a`	Input	First node
`const void*`	`b`	Input	Second node
`ajint`		RETURN	Compare value (-1, 0, +1)

From EMBOSS 4.0.0

Function embGrpOutputGroupsList

Displays a list of groups to an output file handle.

Prototype

void embGrpOutputGroupsList (
      AjPFile outfile,
      const AjPList groupslist,
      AjBool showprogs,
      AjBool html,
      AjBool showkey,
      const AjPStr package
);

Type Name Read/Write Description

AjPFile outfile Modify Output file handle

const AjPList groupslist Input List of groups to be displayed

AjBool showprogs Input If True, display the programs in each group

AjBool html Input If True, format for HTML, else make a simple list

AjBool showkey Input If True, show keywords

const AjPStr package Input Name of current package

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outfile`	Modify	Output file handle
`const AjPList`	`groupslist`	Input	List of groups to be displayed
`AjBool`	`showprogs`	Input	If True, display the programs in each group
`AjBool`	`html`	Input	If True, format for HTML, else make a simple list
`AjBool`	`showkey`	Input	If True, show keywords
`const AjPStr`	`package`	Input	Name of current package
`void`		RETURN

From EMBOSS 2.0.0

Function embGrpOutputProgsList

Displays a list of programs and their descriptions to an output file handle.

Prototype

void embGrpOutputProgsList (
      AjPFile outfile,
      const AjPList progslist,
      AjBool html,
      AjBool showkey,
      const AjPStr package
);

Type Name Read/Write Description

AjPFile outfile Modify Output file handle

const AjPList progslist Input List of programs to be displayed

AjBool html Input If True, format for HTML, else make a simple list

AjBool showkey Input Show keywords in output

const AjPStr package Input Name of current package

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outfile`	Modify	Output file handle
`const AjPList`	`progslist`	Input	List of programs to be displayed
`AjBool`	`html`	Input	If True, format for HTML, else make a simple list
`AjBool`	`showkey`	Input	Show keywords in output
`const AjPStr`	`package`	Input	Name of current package
`void`		RETURN

From EMBOSS 2.0.0

Function embGrpGroupsListDel

Destructor for a groups list

Prototype

void embGrpGroupsListDel (
      AjPList* groupslist
);

Type Name Read/Write Description

AjPList* groupslist Delete List of groups to be destroyed

void RETURN

Type	Name	Read/Write	Description
`AjPList*`	`groupslist`	Delete	List of groups to be destroyed
`void`		RETURN

From EMBOSS 2.0.0

Function embGrpProgsListDel

Destructor for a groups list

Prototype

void embGrpProgsListDel (
      AjPList* progslist
);

Type Name Read/Write Description

AjPList* progslist Delete List of programs to be destroyed

void RETURN

Type	Name	Read/Write	Description
`AjPList*`	`progslist`	Delete	List of programs to be destroyed
`void`		RETURN

From EMBOSS 4.0.0

Function embGrpProgDel

Destructor for a program node

Prototype

void embGrpProgDel (
      EmbPGroupProg* Pgl
);

Type Name Read/Write Description

EmbPGroupProg* Pgl Delete Program node

void RETURN

Type	Name	Read/Write	Description
`EmbPGroupProg*`	`Pgl`	Delete	Program node
`void`		RETURN

From EMBOSS 6.4.0

Function embGrpRelationsListDel

Destructor for a relations list

Prototype

void embGrpRelationsListDel (
      AjPList* relslist
);

Type Name Read/Write Description

AjPList* relslist Delete List of relations to be destroyed

void RETURN

Type	Name	Read/Write	Description
`AjPList*`	`relslist`	Delete	List of relations to be destroyed
`void`		RETURN

From EMBOSS 6.4.0

Function embGrpKeySearchProgs

Searches a list of groups and programs for (partial) matches to a keyword

Prototype

void embGrpKeySearchProgs (
      AjPList newlist,
      const AjPList glist,
      const AjPStr key,
      AjBool all
);

Type	Name	Read/Write	Description
`AjPList`	`newlist`	Output	List of matching EmbPGroupProg struct returned
`const AjPList`	`glist`	Input	List of EmbPGroupProg struct to search through
`const AjPStr`	`key`	Input	String to search for
`AjBool`	`all`	Input	Match all words in key search string
`void`		RETURN

From EMBOSS 2.0.0

Function embGrpSearchProgsEdam

Searches a list of groups and programs for (partial) matches to EDAM topic terms

Prototype

void embGrpSearchProgsEdam (
      AjPList newlist,
      const AjPList glist,
      const AjPStr query,
      const char* namespace,
      AjBool sensitive,
      AjBool subclasses,
      AjBool obsolete
);

Type Name Read/Write Description

AjPList newlist Output List of matching EmbPGroupProg struct returned

const AjPList glist Input List of EmbPGroupProg struct to search through

const AjPStr query Input String(s) to search for

const char* namespace Input EDAM namespace to search

AjBool sensitive Input Match EDAM definitions

AjBool subclasses Input Match EDAM subclasses

AjBool obsolete Input Match EDAM obsolete terms

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`newlist`	Output	List of matching EmbPGroupProg struct returned
`const AjPList`	`glist`	Input	List of EmbPGroupProg struct to search through
`const AjPStr`	`query`	Input	String(s) to search for
`const char*`	`namespace`	Input	EDAM namespace to search
`AjBool`	`sensitive`	Input	Match EDAM definitions
`AjBool`	`subclasses`	Input	Match EDAM subclasses
`AjBool`	`obsolete`	Input	Match EDAM obsolete terms
`void`		RETURN

From EMBOSS 6.4.0

Function embGrpKeySearchSeeAlso

Takes an application name and returns a list of the groups that the application belongs to and a list of the applications that are in those groups.

Prototype

void embGrpKeySearchSeeAlso (
      AjPList newlist,
      AjPList* appgroups,
      AjPStr* package,
      const AjPList alpha,
      const AjPList glist,
      const AjPStr key
);

Type Name Read/Write Description

AjPList newlist Modify List of application groups EmbPGroupTop returned

AjPList* appgroups Output List of EmbPGroupTop groups of programs returned

AjPStr* package Output List of EmbPGroupTop groups of programs

const AjPList alpha Input List of EmbPGroupProg struct to search through

const AjPList glist Input List of EmbPGroupTop struct to search through

const AjPStr key Input program name to search for

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`newlist`	Modify	List of application groups EmbPGroupTop returned
`AjPList*`	`appgroups`	Output	List of EmbPGroupTop groups of programs returned
`AjPStr*`	`package`	Output	List of EmbPGroupTop groups of programs
`const AjPList`	`alpha`	Input	List of EmbPGroupProg struct to search through
`const AjPList`	`glist`	Input	List of EmbPGroupTop struct to search through
`const AjPStr`	`key`	Input	program name to search for
`void`		RETURN

From EMBOSS 2.0.0

Function embGrpProgsMakeUnique

Takes a sorted EmbPGroupProg list and ensures that there are no duplicate group or application names in that list.

Prototype

void embGrpProgsMakeUnique (
      AjPList list
);

Type Name Read/Write Description

AjPList list Modify List of application GPnode returned

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`list`	Modify	List of application GPnode returned
`void`		RETURN

From EMBOSS 4.0.0

Function embGrpGroupMakeUnique

Takes a sorted EmbPGroupTop list and ensures that there are no duplicate group or application names in that list.

Prototype

void embGrpGroupMakeUnique (
      AjPList list
);

Type Name Read/Write Description

AjPList list Modify List of application GPnode returned

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`list`	Modify	List of application GPnode returned
`void`		RETURN

From EMBOSS 4.0.0

Function embGrpExit

Cleanup program group internals on exit

Prototype

void embGrpExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0