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
);

TypeNameRead/WriteDescription
AjPPatlistSeqplistModifyPattern list
const AjPStrnameInputName of the pattern
const AjPStrpatInputPattern as string
ajuintmismatchInputmismatch value
AjPPatternSeq RETURNNew 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
);

TypeNameRead/WriteDescription
AjPPatlistRegexplistModifyRegular expression pattern list
const AjPStrnameInputName of the pattern
const AjPStrpatInputPattern as string
AjPPatternRegex RETURNNew regular expression pattern object

From EMBOSS 4.0.0


Function ajPatternRegexDel

Destructor for a regular expression pattern object

Prototype

void ajPatternRegexDel (
      AjPPatternRegex* pthys
);

TypeNameRead/WriteDescription
AjPPatternRegex*pthysDeletePattern object reference
void RETURN

From EMBOSS 4.0.0


Function ajPatternSeqDel

Destructor for a pattern object

Prototype

void ajPatternSeqDel (
      AjPPatternSeq* pthys
);

TypeNameRead/WriteDescription
AjPPatternSeq*pthysDeletePattern object reference
void RETURN

From EMBOSS 4.0.0


Function ajPatternSeqGetName

Returns the name of the pattern.

Prototype

const AjPStr ajPatternSeqGetName (
      const AjPPatternSeq thys
);

TypeNameRead/WriteDescription
const AjPPatternSeqthysInputPattern
const AjPStr RETURNName 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
);

TypeNameRead/WriteDescription
const AjPPatternRegexthysInputPattern
const AjPStr RETURNName 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
);

TypeNameRead/WriteDescription
const AjPPatternSeqthysInputPattern
const AjPStr RETURNPattern. Real pointer in structure.

From EMBOSS 4.0.0


Function ajPatternRegexGetPattern

Returns pattern in string format.

Prototype

const AjPStr ajPatternRegexGetPattern (
      const AjPPatternRegex thys
);

TypeNameRead/WriteDescription
const AjPPatternRegexthysInputPattern
const AjPStr RETURNPattern. Real pointer in structure.

From EMBOSS 4.0.0


Function ajPatternSeqGetCompiled

Returns void pointer to compiled pattern.

Prototype

AjPPatComp ajPatternSeqGetCompiled (
      const AjPPatternSeq thys
);

TypeNameRead/WriteDescription
const AjPPatternSeqthysInputPattern
AjPPatComp RETURNReference 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
);

TypeNameRead/WriteDescription
const AjPPatternRegexthysInputPattern
AjPRegexp RETURNReference 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
);

TypeNameRead/WriteDescription
const AjPPatternSeqthysInputPattern
AjBool RETURNajTrue for a protein pattern

From EMBOSS 4.0.0


Function ajPatternRegexGetType

Returns the type of the pattern.

Prototype

ajuint ajPatternRegexGetType (
      const AjPPatternRegex thys
);

TypeNameRead/WriteDescription
const AjPPatternRegexthysInputPattern
ajuint RETURNType of the pattern.

From EMBOSS 4.0.0


Function ajPatternSeqGetMismatch

Returns the mismatch of the pattern.

Prototype

ajuint ajPatternSeqGetMismatch (
      const AjPPatternSeq thys
);

TypeNameRead/WriteDescription
const AjPPatternSeqthysInputPattern
ajuint RETURNMismatch value of the pattern.

From EMBOSS 4.0.0


Function ajPatternSeqSetCompiled

Sets the compiled pattern

Prototype

void ajPatternSeqSetCompiled (
      AjPPatternSeq thys,
      void* pat
);

TypeNameRead/WriteDescription
AjPPatternSeqthysModifyPattern
void*patModifyCompiled pattern
void RETURN

From EMBOSS 4.0.0


Function ajPatternRegexSetCompiled

Sets the compiled pattern

Prototype

void ajPatternRegexSetCompiled (
      AjPPatternRegex thys,
      AjPRegexp pat
);

TypeNameRead/WriteDescription
AjPPatternRegexthysModifyPattern
AjPRegexppatModifyCompiled pattern
void RETURN

From EMBOSS 4.0.0


Function ajPatternSeqDebug

Constructor for a pattern list object

Prototype

void ajPatternSeqDebug (
      const AjPPatternSeq pat
);

TypeNameRead/WriteDescription
const AjPPatternSeqpatInputPattern object
void RETURN

From EMBOSS 4.0.0


Function ajPatternRegexDebug

Constructor for a pattern list object

Prototype

void ajPatternRegexDebug (
      const AjPPatternRegex pat
);

TypeNameRead/WriteDescription
const AjPPatternRegexpatInputPattern object
void RETURN

From EMBOSS 4.0.0


Function ajPatlistRegexNew

Constructor for a pattern list object

Prototype

AjPPatlistRegex ajPatlistRegexNew (
      void
);

TypeNameRead/WriteDescription
AjPPatlistRegex RETURNNew 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
);

TypeNameRead/WriteDescription
ajuinttypeInputtype value
AjPPatlistRegex RETURNNew pattern list object

From EMBOSS 4.0.0


Function ajPatlistSeqNew

Constructor for a pattern list object. Defaults to protein.

Prototype

AjPPatlistSeq ajPatlistSeqNew (
      void
);

TypeNameRead/WriteDescription
AjPPatlistSeq RETURNNew pattern list object

From EMBOSS 4.0.0


Function ajPatlistSeqNewType

Constructor for a pattern list object

Prototype

AjPPatlistSeq ajPatlistSeqNewType (
      AjBool type
);

TypeNameRead/WriteDescription
AjBooltypeInputTrue for a protein pattern
AjPPatlistSeq RETURNNew pattern list object

From EMBOSS 4.0.0


Function ajPatlistRegexDel

Destructor for a pattern list object

Prototype

void ajPatlistRegexDel (
      AjPPatlistRegex* pthys
);

TypeNameRead/WriteDescription
AjPPatlistRegex*pthysDeletePattern list object reference
void RETURN

From EMBOSS 4.0.0


Function ajPatlistSeqDel

Destructor for a pattern list object

Prototype

void ajPatlistSeqDel (
      AjPPatlistSeq* pthys
);

TypeNameRead/WriteDescription
AjPPatlistSeq*pthysDeletePattern 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
);

TypeNameRead/WriteDescription
const AjPStrpatspecInputPattern specification
const AjPStrpatnameInputDefault pattern name prefix
const AjPStrfmtInputPattern file format
AjBoolproteinInputajTrue for protein patterns
ajuintmismatchesInputdefault number of mismatches
AjPPatlistSeq RETURNPattern 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
);

TypeNameRead/WriteDescription
const AjPStrpatspecInputName of the file with patterns
const AjPStrpatnameInputDefault pattern name prefix
const AjPStrfmtInputPattern file format
ajuinttypeInputType of the patterns
AjBoolupperInputConvert to upper case
AjBoollowerInputConvert to lower case
AjPPatlistRegex RETURNPattern list

From EMBOSS 4.0.0


Function ajPatlistSeqGetSize

Gets number of patterns from list.

Prototype

ajuint ajPatlistSeqGetSize (
      const AjPPatlistSeq thys
);

TypeNameRead/WriteDescription
const AjPPatlistSeqthysInputPattern list object
ajuint RETURNNumber of patterns

From EMBOSS 4.0.0


Function ajPatlistRegexGetSize

Gets number of patterns from list.

Prototype

ajuint ajPatlistRegexGetSize (
      const AjPPatlistRegex thys
);

TypeNameRead/WriteDescription
const AjPPatlistRegexthysInputPattern list object
ajuint RETURNNumber of patterns

From EMBOSS 4.0.0


Function ajPatlistSeqGetNext

Gets next available pattern from list.

Prototype

AjBool ajPatlistSeqGetNext (
      AjPPatlistSeq thys,
      AjPPatternSeq* pattern
);

TypeNameRead/WriteDescription
AjPPatlistSeqthysModifyPattern list object
AjPPatternSeq*patternOutputPattern object reference
AjBool RETURNajTrue 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
);

TypeNameRead/WriteDescription
AjPPatlistRegexthysModifyPattern list object
AjPPatternRegex*patternOutputPattern object reference
AjBool RETURNajTrue if there was next object

From EMBOSS 4.0.0


Function ajPatlistRegexRewind

Resets the pattern list iteration.

Prototype

void ajPatlistRegexRewind (
      AjPPatlistRegex thys
);

TypeNameRead/WriteDescription
AjPPatlistRegexthysModifyPattern list object reference
void RETURN

From EMBOSS 4.0.0


Function ajPatlistSeqRewind

Resets the pattern list iteration.

Prototype

void ajPatlistSeqRewind (
      AjPPatlistSeq thys
);

TypeNameRead/WriteDescription
AjPPatlistSeqthysModifyPattern 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
);

TypeNameRead/WriteDescription
AjPPatlistRegexthysModifyPattern 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
);

TypeNameRead/WriteDescription
AjPPatlistSeqthysModifyPattern 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
);

TypeNameRead/WriteDescription
AjPPatlistSeqthysModifyPattern list object reference
AjPPatternSeqpatModifyPattern to be added
void RETURN

From EMBOSS 4.0.0


Function ajPatlistAddRegex

Adds pattern into patternlist

Prototype

void ajPatlistAddRegex (
      AjPPatlistRegex thys,
      AjPPatternRegex pat
);

TypeNameRead/WriteDescription
AjPPatlistRegexthysModifyPattern list object reference
AjPPatternRegexpatModifyPattern to be added
void RETURN

From EMBOSS 4.0.0


Function ajPatCompNew

Create prosite pattern structure.

Prototype

AjPPatComp ajPatCompNew (
      void
);

TypeNameRead/WriteDescription
AjPPatComp RETURNpattern structure

From EMBOSS 4.1.0


Function ajPatCompDel

Delete prosite pattern structure.

Prototype

void ajPatCompDel (
      AjPPatComp* pthys
);

TypeNameRead/WriteDescription
AjPPatComp*pthysDeleteProsite 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
);

TypeNameRead/WriteDescription
const AjPStrtypeInputRegular expression type
ajuint RETURNType 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
);

TypeNameRead/WriteDescription
AjPPatlistRegexplistModifyPattern list object
AjPStr*PdocOutputFormatted string
ajuint RETURNNumber of patterns

From EMBOSS 4.0.0


Function ajPatlistSeqDoc

Documents patterns to a formatted string

Prototype

ajuint ajPatlistSeqDoc (
      AjPPatlistSeq plist,
      AjPStr* Pdoc
);

TypeNameRead/WriteDescription
AjPPatlistSeqplistModifyPattern list object
AjPStr*PdocOutputFormatted string
ajuint RETURNNumber of patterns

From EMBOSS 4.0.0