ajpat.c

Function ajPatternSeqNewList

Constructor for a sequence pattern object. Sets all but compiled object. That is set with search function. Adds the pattern to a pattern list.

Prototype

AjPPatternSeq ajPatternSeqNewList (
      AjPPatlistSeq plist,
      const AjPStr name,
      const AjPStr pat,
      ajuint mismatch
);

Type Name Read/Write Description

AjPPatlistSeq plist Modify Pattern list

const AjPStr name Input Name of the pattern

const AjPStr pat Input Pattern as string

ajuint mismatch Input mismatch value

AjPPatternSeq RETURN New pattern object

Type	Name	Read/Write	Description
`AjPPatlistSeq`	`plist`	Modify	Pattern list
`const AjPStr`	`name`	Input	Name of the pattern
`const AjPStr`	`pat`	Input	Pattern as string
`ajuint`	`mismatch`	Input	mismatch value
`AjPPatternSeq`		RETURN	New pattern object

From EMBOSS 4.0.0

Function ajPatternRegexNewList

Constructor for a pattern object. Sets all but compiled object. That is set with search function. Adds the pattern to a pattern list.

Prototype

AjPPatternRegex ajPatternRegexNewList (
      AjPPatlistRegex plist,
      const AjPStr name,
      const AjPStr pat
);

Type Name Read/Write Description

AjPPatlistRegex plist Modify Regular expression pattern list

const AjPStr name Input Name of the pattern

const AjPStr pat Input Pattern as string

AjPPatternRegex RETURN New regular expression pattern object

Type	Name	Read/Write	Description
`AjPPatlistRegex`	`plist`	Modify	Regular expression pattern list
`const AjPStr`	`name`	Input	Name of the pattern
`const AjPStr`	`pat`	Input	Pattern as string
`AjPPatternRegex`		RETURN	New regular expression pattern object

From EMBOSS 4.0.0

Function ajPatternRegexDel

Destructor for a regular expression pattern object

Prototype

void ajPatternRegexDel (
      AjPPatternRegex* pthys
);

Type Name Read/Write Description

AjPPatternRegex* pthys Delete Pattern object reference

void RETURN

Type	Name	Read/Write	Description
`AjPPatternRegex*`	`pthys`	Delete	Pattern object reference
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatternSeqDel

Destructor for a pattern object

Prototype

void ajPatternSeqDel (
      AjPPatternSeq* pthys
);

Type Name Read/Write Description

AjPPatternSeq* pthys Delete Pattern object reference

void RETURN

Type	Name	Read/Write	Description
`AjPPatternSeq*`	`pthys`	Delete	Pattern object reference
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatternSeqGetName

Returns the name of the pattern.

Prototype

const AjPStr ajPatternSeqGetName (
      const AjPPatternSeq thys
);

Type Name Read/Write Description

const AjPPatternSeq thys Input Pattern

const AjPStr RETURN Name of the pattern. Real pointer in structure.

Type	Name	Read/Write	Description
`const AjPPatternSeq`	`thys`	Input	Pattern
`const AjPStr`		RETURN	Name of the pattern. Real pointer in structure.

From EMBOSS 4.0.0

Function ajPatternRegexGetName

Returns the name of the pattern.

Prototype

const AjPStr ajPatternRegexGetName (
      const AjPPatternRegex thys
);

Type Name Read/Write Description

const AjPPatternRegex thys Input Pattern

const AjPStr RETURN Name of the pattern. Real pointer in structure.

Type	Name	Read/Write	Description
`const AjPPatternRegex`	`thys`	Input	Pattern
`const AjPStr`		RETURN	Name of the pattern. Real pointer in structure.

From EMBOSS 4.0.0

Function ajPatternSeqGetPattern

Returns pattern in string format.

Prototype

const AjPStr ajPatternSeqGetPattern (
      const AjPPatternSeq thys
);

Type Name Read/Write Description

const AjPPatternSeq thys Input Pattern

const AjPStr RETURN Pattern. Real pointer in structure.

Type	Name	Read/Write	Description
`const AjPPatternSeq`	`thys`	Input	Pattern
`const AjPStr`		RETURN	Pattern. Real pointer in structure.

From EMBOSS 4.0.0

Function ajPatternRegexGetPattern

Returns pattern in string format.

Prototype

const AjPStr ajPatternRegexGetPattern (
      const AjPPatternRegex thys
);

Type Name Read/Write Description

const AjPPatternRegex thys Input Pattern

const AjPStr RETURN Pattern. Real pointer in structure.

Type	Name	Read/Write	Description
`const AjPPatternRegex`	`thys`	Input	Pattern
`const AjPStr`		RETURN	Pattern. Real pointer in structure.

From EMBOSS 4.0.0

Function ajPatternSeqGetCompiled

Returns void pointer to compiled pattern.

Prototype

AjPPatComp ajPatternSeqGetCompiled (
      const AjPPatternSeq thys
);

Type Name Read/Write Description

const AjPPatternSeq thys Input Pattern

AjPPatComp RETURN Reference for compiled pattern

Type	Name	Read/Write	Description
`const AjPPatternSeq`	`thys`	Input	Pattern
`AjPPatComp`		RETURN	Reference for compiled pattern

From EMBOSS 4.0.0

Function ajPatternRegexGetCompiled

Returns void pointer to compiled pattern. Compiles expression if not yet done.

Prototype

AjPRegexp ajPatternRegexGetCompiled (
      const AjPPatternRegex thys
);

Type Name Read/Write Description

const AjPPatternRegex thys Input Pattern

AjPRegexp RETURN Reference for compiled pattern

Type	Name	Read/Write	Description
`const AjPPatternRegex`	`thys`	Input	Pattern
`AjPRegexp`		RETURN	Reference for compiled pattern

From EMBOSS 4.0.0

Function ajPatternSeqGetProtein

Returns true if the pattern is for a protein sequence.

Prototype

AjBool ajPatternSeqGetProtein (
      const AjPPatternSeq thys
);

Type Name Read/Write Description

const AjPPatternSeq thys Input Pattern

AjBool RETURN ajTrue for a protein pattern

Type	Name	Read/Write	Description
`const AjPPatternSeq`	`thys`	Input	Pattern
`AjBool`		RETURN	ajTrue for a protein pattern

From EMBOSS 4.0.0

Function ajPatternRegexGetType

Returns the type of the pattern.

Prototype

ajuint ajPatternRegexGetType (
      const AjPPatternRegex thys
);

Type Name Read/Write Description

const AjPPatternRegex thys Input Pattern

ajuint RETURN Type of the pattern.

Type	Name	Read/Write	Description
`const AjPPatternRegex`	`thys`	Input	Pattern
`ajuint`		RETURN	Type of the pattern.

From EMBOSS 4.0.0

Function ajPatternSeqGetMismatch

Returns the mismatch of the pattern.

Prototype

ajuint ajPatternSeqGetMismatch (
      const AjPPatternSeq thys
);

Type Name Read/Write Description

const AjPPatternSeq thys Input Pattern

ajuint RETURN Mismatch value of the pattern.

Type	Name	Read/Write	Description
`const AjPPatternSeq`	`thys`	Input	Pattern
`ajuint`		RETURN	Mismatch value of the pattern.

From EMBOSS 4.0.0

Function ajPatternSeqSetCompiled

Sets the compiled pattern

Prototype

void ajPatternSeqSetCompiled (
      AjPPatternSeq thys,
      void* pat
);

Type Name Read/Write Description

AjPPatternSeq thys Modify Pattern

void* pat Modify Compiled pattern

void RETURN

Type	Name	Read/Write	Description
`AjPPatternSeq`	`thys`	Modify	Pattern
`void*`	`pat`	Modify	Compiled pattern
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatternRegexSetCompiled

Sets the compiled pattern

Prototype

void ajPatternRegexSetCompiled (
      AjPPatternRegex thys,
      AjPRegexp pat
);

Type Name Read/Write Description

AjPPatternRegex thys Modify Pattern

AjPRegexp pat Modify Compiled pattern

void RETURN

Type	Name	Read/Write	Description
`AjPPatternRegex`	`thys`	Modify	Pattern
`AjPRegexp`	`pat`	Modify	Compiled pattern
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatternSeqDebug

Constructor for a pattern list object

Prototype

void ajPatternSeqDebug (
      const AjPPatternSeq pat
);

Type Name Read/Write Description

const AjPPatternSeq pat Input Pattern object

void RETURN

Type	Name	Read/Write	Description
`const AjPPatternSeq`	`pat`	Input	Pattern object
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatternRegexDebug

Constructor for a pattern list object

Prototype

void ajPatternRegexDebug (
      const AjPPatternRegex pat
);

Type Name Read/Write Description

const AjPPatternRegex pat Input Pattern object

void RETURN

Type	Name	Read/Write	Description
`const AjPPatternRegex`	`pat`	Input	Pattern object
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistRegexNew

Constructor for a pattern list object

Prototype

AjPPatlistRegex ajPatlistRegexNew (
      void
);

Type Name Read/Write Description

AjPPatlistRegex RETURN New pattern list object

Type	Name	Read/Write	Description
`AjPPatlistRegex`		RETURN	New pattern list object

From EMBOSS 4.0.0

Function ajPatlistRegexNewType

Constructor for a pattern list object with a specified type

Prototype

AjPPatlistRegex ajPatlistRegexNewType (
      ajuint type
);

Type Name Read/Write Description

ajuint type Input type value

AjPPatlistRegex RETURN New pattern list object

Type	Name	Read/Write	Description
`ajuint`	`type`	Input	type value
`AjPPatlistRegex`		RETURN	New pattern list object

From EMBOSS 4.0.0

Function ajPatlistSeqNew

Constructor for a pattern list object. Defaults to protein.

Prototype

AjPPatlistSeq ajPatlistSeqNew (
      void
);

Type Name Read/Write Description

AjPPatlistSeq RETURN New pattern list object

Type	Name	Read/Write	Description
`AjPPatlistSeq`		RETURN	New pattern list object

From EMBOSS 4.0.0

Function ajPatlistSeqNewType

Constructor for a pattern list object

Prototype

AjPPatlistSeq ajPatlistSeqNewType (
      AjBool type
);

Type Name Read/Write Description

AjBool type Input True for a protein pattern

AjPPatlistSeq RETURN New pattern list object

Type	Name	Read/Write	Description
`AjBool`	`type`	Input	True for a protein pattern
`AjPPatlistSeq`		RETURN	New pattern list object

From EMBOSS 4.0.0

Function ajPatlistRegexDel

Destructor for a pattern list object

Prototype

void ajPatlistRegexDel (
      AjPPatlistRegex* pthys
);

Type Name Read/Write Description

AjPPatlistRegex* pthys Delete Pattern list object reference

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistRegex*`	`pthys`	Delete	Pattern list object reference
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistSeqDel

Destructor for a pattern list object

Prototype

void ajPatlistSeqDel (
      AjPPatlistSeq* pthys
);

Type Name Read/Write Description

AjPPatlistSeq* pthys Delete Pattern list object reference

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistSeq*`	`pthys`	Delete	Pattern list object reference
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistSeqRead

Parses a file into pattern list object. If there is not mismatch value on pattern in file, it is assumed to be 0.

Prototype

AjPPatlistSeq ajPatlistSeqRead (
      const AjPStr patspec,
      const AjPStr patname,
      const AjPStr fmt,
      AjBool protein,
      ajuint mismatches
);

Type Name Read/Write Description

const AjPStr patspec Input Pattern specification

const AjPStr patname Input Default pattern name prefix

const AjPStr fmt Input Pattern file format

AjBool protein Input ajTrue for protein patterns

ajuint mismatches Input default number of mismatches

AjPPatlistSeq RETURN Pattern list

Type	Name	Read/Write	Description
`const AjPStr`	`patspec`	Input	Pattern specification
`const AjPStr`	`patname`	Input	Default pattern name prefix
`const AjPStr`	`fmt`	Input	Pattern file format
`AjBool`	`protein`	Input	ajTrue for protein patterns
`ajuint`	`mismatches`	Input	default number of mismatches
`AjPPatlistSeq`		RETURN	Pattern list

From EMBOSS 4.0.0

Function ajPatlistRegexRead

Parses a file of regular expressions into a pattern list object.

Prototype

AjPPatlistRegex ajPatlistRegexRead (
      const AjPStr patspec,
      const AjPStr patname,
      const AjPStr fmt,
      ajuint type,
      AjBool upper,
      AjBool lower
);

Type Name Read/Write Description

const AjPStr patspec Input Name of the file with patterns

const AjPStr patname Input Default pattern name prefix

const AjPStr fmt Input Pattern file format

ajuint type Input Type of the patterns

AjBool upper Input Convert to upper case

AjBool lower Input Convert to lower case

AjPPatlistRegex RETURN Pattern list

Type	Name	Read/Write	Description
`const AjPStr`	`patspec`	Input	Name of the file with patterns
`const AjPStr`	`patname`	Input	Default pattern name prefix
`const AjPStr`	`fmt`	Input	Pattern file format
`ajuint`	`type`	Input	Type of the patterns
`AjBool`	`upper`	Input	Convert to upper case
`AjBool`	`lower`	Input	Convert to lower case
`AjPPatlistRegex`		RETURN	Pattern list

From EMBOSS 4.0.0

Function ajPatlistSeqGetSize

Gets number of patterns from list.

Prototype

ajuint ajPatlistSeqGetSize (
      const AjPPatlistSeq thys
);

Type Name Read/Write Description

const AjPPatlistSeq thys Input Pattern list object

ajuint RETURN Number of patterns

Type	Name	Read/Write	Description
`const AjPPatlistSeq`	`thys`	Input	Pattern list object
`ajuint`		RETURN	Number of patterns

From EMBOSS 4.0.0

Function ajPatlistRegexGetSize

Gets number of patterns from list.

Prototype

ajuint ajPatlistRegexGetSize (
      const AjPPatlistRegex thys
);

Type Name Read/Write Description

const AjPPatlistRegex thys Input Pattern list object

ajuint RETURN Number of patterns

Type	Name	Read/Write	Description
`const AjPPatlistRegex`	`thys`	Input	Pattern list object
`ajuint`		RETURN	Number of patterns

From EMBOSS 4.0.0

Function ajPatlistSeqGetNext

Gets next available pattern from list.

Prototype

AjBool ajPatlistSeqGetNext (
      AjPPatlistSeq thys,
      AjPPatternSeq* pattern
);

Type Name Read/Write Description

AjPPatlistSeq thys Modify Pattern list object

AjPPatternSeq* pattern Output Pattern object reference

AjBool RETURN ajTrue if there was next object

Type	Name	Read/Write	Description
`AjPPatlistSeq`	`thys`	Modify	Pattern list object
`AjPPatternSeq*`	`pattern`	Output	Pattern object reference
`AjBool`		RETURN	ajTrue if there was next object

From EMBOSS 4.0.0

Function ajPatlistRegexGetNext

Gets next available pattern from list.

Prototype

AjBool ajPatlistRegexGetNext (
      AjPPatlistRegex thys,
      AjPPatternRegex* pattern
);

Type Name Read/Write Description

AjPPatlistRegex thys Modify Pattern list object

AjPPatternRegex* pattern Output Pattern object reference

AjBool RETURN ajTrue if there was next object

Type	Name	Read/Write	Description
`AjPPatlistRegex`	`thys`	Modify	Pattern list object
`AjPPatternRegex*`	`pattern`	Output	Pattern object reference
`AjBool`		RETURN	ajTrue if there was next object

From EMBOSS 4.0.0

Function ajPatlistRegexRewind

Resets the pattern list iteration.

Prototype

void ajPatlistRegexRewind (
      AjPPatlistRegex thys
);

Type Name Read/Write Description

AjPPatlistRegex thys Modify Pattern list object reference

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistRegex`	`thys`	Modify	Pattern list object reference
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistSeqRewind

Resets the pattern list iteration.

Prototype

void ajPatlistSeqRewind (
      AjPPatlistSeq thys
);

Type Name Read/Write Description

AjPPatlistSeq thys Modify Pattern list object reference

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistSeq`	`thys`	Modify	Pattern list object reference
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistRegexRemoveCurrent

Removes current pattern from pattern list. If looping has not started or pattern list has just been rewound then nothing is removed.

Prototype

void ajPatlistRegexRemoveCurrent (
      AjPPatlistRegex thys
);

Type Name Read/Write Description

AjPPatlistRegex thys Modify Pattern list from which to remove

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistRegex`	`thys`	Modify	Pattern list from which to remove
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistSeqRemoveCurrent

Removes current pattern from pattern list. If looping has not started or pattern list has just been rewound then nothing is removed.

Prototype

void ajPatlistSeqRemoveCurrent (
      AjPPatlistSeq thys
);

Type Name Read/Write Description

AjPPatlistSeq thys Modify Pattern list from which to remove

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistSeq`	`thys`	Modify	Pattern list from which to remove
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistAddSeq

Adds pattern into patternlist

Prototype

void ajPatlistAddSeq (
      AjPPatlistSeq thys,
      AjPPatternSeq pat
);

Type Name Read/Write Description

AjPPatlistSeq thys Modify Pattern list object reference

AjPPatternSeq pat Modify Pattern to be added

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistSeq`	`thys`	Modify	Pattern list object reference
`AjPPatternSeq`	`pat`	Modify	Pattern to be added
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatlistAddRegex

Adds pattern into patternlist

Prototype

void ajPatlistAddRegex (
      AjPPatlistRegex thys,
      AjPPatternRegex pat
);

Type Name Read/Write Description

AjPPatlistRegex thys Modify Pattern list object reference

AjPPatternRegex pat Modify Pattern to be added

void RETURN

Type	Name	Read/Write	Description
`AjPPatlistRegex`	`thys`	Modify	Pattern list object reference
`AjPPatternRegex`	`pat`	Modify	Pattern to be added
`void`		RETURN

From EMBOSS 4.0.0

Function ajPatCompNew

Create prosite pattern structure.

Prototype

AjPPatComp ajPatCompNew (
      void
);

Type Name Read/Write Description

AjPPatComp RETURN pattern structure

Type	Name	Read/Write	Description
`AjPPatComp`		RETURN	pattern structure

From EMBOSS 4.1.0

Function ajPatCompDel

Delete prosite pattern structure.

Prototype

void ajPatCompDel (
      AjPPatComp* pthys
);

Type Name Read/Write Description

AjPPatComp* pthys Delete Prosite pattern structure

void RETURN

Type	Name	Read/Write	Description
`AjPPatComp*`	`pthys`	Delete	Prosite pattern structure
`void`		RETURN

From EMBOSS 4.1.0

Function ajPatternRegexType

Returns type associated with a named type of regular expression

Prototype

ajuint ajPatternRegexType (
      const AjPStr type
);

Type Name Read/Write Description

const AjPStr type Input Regular expression type

ajuint RETURN Type number, defaults to 0 (string)

Type	Name	Read/Write	Description
`const AjPStr`	`type`	Input	Regular expression type
`ajuint`		RETURN	Type number, defaults to 0 (string)

From EMBOSS 4.0.0

Function ajPatlistRegexDoc

Documents patterns to a formatted string

Prototype

ajuint ajPatlistRegexDoc (
      AjPPatlistRegex plist,
      AjPStr* Pdoc
);

Type Name Read/Write Description

AjPPatlistRegex plist Modify Pattern list object

AjPStr* Pdoc Output Formatted string

ajuint RETURN Number of patterns

Type	Name	Read/Write	Description
`AjPPatlistRegex`	`plist`	Modify	Pattern list object
`AjPStr*`	`Pdoc`	Output	Formatted string
`ajuint`		RETURN	Number of patterns

From EMBOSS 4.0.0

Function ajPatlistSeqDoc

Documents patterns to a formatted string

Prototype

ajuint ajPatlistSeqDoc (
      AjPPatlistSeq plist,
      AjPStr* Pdoc
);

Type Name Read/Write Description

AjPPatlistSeq plist Modify Pattern list object

AjPStr* Pdoc Output Formatted string

ajuint RETURN Number of patterns

Type	Name	Read/Write	Description
`AjPPatlistSeq`	`plist`	Modify	Pattern list object
`AjPStr*`	`Pdoc`	Output	Formatted string
`ajuint`		RETURN	Number of patterns

From EMBOSS 4.0.0