embpat.c

Function embPatSeqCreateRegExp

Create a regular expression for a string and substitute the chars for Nucleotides or proteins as needed.

Prototype

AjPStr embPatSeqCreateRegExp (
      const AjPStr thys,
      AjBool protein
);

Type Name Read/Write Description

const AjPStr thys Input string to create reg expr from.

AjBool protein Input is it a protein.

AjPStr RETURN the new regular expression.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	string to create reg expr from.
`AjBool`	`protein`	Input	is it a protein.
`AjPStr`		RETURN	the new regular expression.

From EMBOSS 1.0.0

Function embPatSeqCreateRegExpC

Create a regular expression for a string and substitute the chars for Nucleotides or proteins as needed.

Prototype

AjPStr embPatSeqCreateRegExpC (
      const char* ptr,
      AjBool protein
);

Type Name Read/Write Description

const char* ptr Input text to create reg expr from.

AjBool protein Input is it a protein.

AjPStr RETURN the new regular expression.

Type	Name	Read/Write	Description
`const char*`	`ptr`	Input	text to create reg expr from.
`AjBool`	`protein`	Input	is it a protein.
`AjPStr`		RETURN	the new regular expression.

From EMBOSS 1.0.0

Function embPatSeqMatchFind

Find all the regular expression matches of reg in the string string.

Prototype

EmbPPatMatch embPatSeqMatchFind (
      const AjPSeq seq,
      const AjPStr reg
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence to be searched.

const AjPStr reg Input regular expression string.

EmbPPatMatch RETURN Results of the pattern matching.

Type	Name	Read/Write	Description
`const AjPSeq`	`seq`	Input	Sequence to be searched.
`const AjPStr`	`reg`	Input	regular expression string.
`EmbPPatMatch`		RETURN	Results of the pattern matching.

From EMBOSS 1.0.0

Function embPatSeqMatchFindC

Find all the regular expression matches of reg in the string string.

Prototype

EmbPPatMatch embPatSeqMatchFindC (
      const AjPSeq seq,
      const char* reg
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence to be searched.

const char* reg Input regular expression text.

EmbPPatMatch RETURN Results of the pattern matching.

Type	Name	Read/Write	Description
`const AjPSeq`	`seq`	Input	Sequence to be searched.
`const char*`	`reg`	Input	regular expression text.
`EmbPPatMatch`		RETURN	Results of the pattern matching.

From EMBOSS 1.0.0

Function embPatMatchFind

Find all the regular expression matches of reg in the string string.

Prototype

EmbPPatMatch embPatMatchFind (
      const AjPStr regexp,
      const AjPStr strng,
      AjBool left,
      AjBool right
);

Type Name Read/Write Description

const AjPStr regexp Input Regular expression string.

const AjPStr strng Input String to be searched.

AjBool left Input has to match the start

AjBool right Input has to match the end

EmbPPatMatch RETURN Results of the pattern matching.

Type	Name	Read/Write	Description
`const AjPStr`	`regexp`	Input	Regular expression string.
`const AjPStr`	`strng`	Input	String to be searched.
`AjBool`	`left`	Input	has to match the start
`AjBool`	`right`	Input	has to match the end
`EmbPPatMatch`		RETURN	Results of the pattern matching.

From EMBOSS 1.0.0

Function embPatMatchFindC

Find all the regular expression matches of reg in the string string.

Prototype

EmbPPatMatch embPatMatchFindC (
      const AjPStr regexp,
      const char* sptr,
      AjBool left,
      AjBool right
);

Type Name Read/Write Description

const AjPStr regexp Input Regular expression string.

const char* sptr Input String to be searched.

AjBool left Input has to match the start

AjBool right Input has to match the end

EmbPPatMatch RETURN Results of the pattern matching.

Type	Name	Read/Write	Description
`const AjPStr`	`regexp`	Input	Regular expression string.
`const char*`	`sptr`	Input	String to be searched.
`AjBool`	`left`	Input	has to match the start
`AjBool`	`right`	Input	has to match the end
`EmbPPatMatch`		RETURN	Results of the pattern matching.

From EMBOSS 1.0.0

Function embPatMatchGetLen

Returns the length from the pattern match structure for index'th item.

Prototype

ajuint embPatMatchGetLen (
      const EmbPPatMatch data,
      ajuint indexnum
);

Type Name Read/Write Description

const EmbPPatMatch data Input results of match.

ajuint indexnum Input index to structure.

ajuint RETURN returns -1 if not available.

Type	Name	Read/Write	Description
`const EmbPPatMatch`	`data`	Input	results of match.
`ajuint`	`indexnum`	Input	index to structure.
`ajuint`		RETURN	returns -1 if not available.

From EMBOSS 1.0.0

Function embPatMatchGetEnd

Returns the End point for the pattern match structure for index'th item.

Prototype

ajuint embPatMatchGetEnd (
      const EmbPPatMatch data,
      ajuint indexnum
);

Type Name Read/Write Description

const EmbPPatMatch data Input results of match.

ajuint indexnum Input index to structure.

ajuint RETURN returns -1 if not available.

Type	Name	Read/Write	Description
`const EmbPPatMatch`	`data`	Input	results of match.
`ajuint`	`indexnum`	Input	index to structure.
`ajuint`		RETURN	returns -1 if not available.

From EMBOSS 1.0.0

Function embPatMatchGetNumber

Returns the number of pattern matches in the structure.

Prototype

ajuint embPatMatchGetNumber (
      const EmbPPatMatch data
);

Type Name Read/Write Description

const EmbPPatMatch data Input results of match.

ajuint RETURN returns -1 if not available.

Type	Name	Read/Write	Description
`const EmbPPatMatch`	`data`	Input	results of match.
`ajuint`		RETURN	returns -1 if not available.

From EMBOSS 1.0.0

Function embPatMatchGetStart

Returns the start position from the pattern match structure for index'th item.

Prototype

ajuint embPatMatchGetStart (
      const EmbPPatMatch data,
      ajuint indexnum
);

Type Name Read/Write Description

const EmbPPatMatch data Input results of match.

ajuint indexnum Input index to structure.

ajuint RETURN returns -1 if not available.

Type	Name	Read/Write	Description
`const EmbPPatMatch`	`data`	Input	results of match.
`ajuint`	`indexnum`	Input	index to structure.
`ajuint`		RETURN	returns -1 if not available.

From EMBOSS 1.0.0

Function embPatMatchDel

Free all the memory from the pattern match search.

Prototype

void embPatMatchDel (
      EmbPPatMatch* pthis
);

Type Name Read/Write Description

EmbPPatMatch* pthis Delete results to be freed.

void RETURN

Type	Name	Read/Write	Description
`EmbPPatMatch*`	`pthis`	Delete	results to be freed.
`void`		RETURN

From EMBOSS 1.0.0

Function embPatPrositeToRegExp

Convert a prosite pattern to a regular expression

Prototype

AjPStr embPatPrositeToRegExp (
      const AjPStr s
);

Type Name Read/Write Description

const AjPStr s Input prosite pattern

AjPStr RETURN regular expression

Type	Name	Read/Write	Description
`const AjPStr`	`s`	Input	prosite pattern
`AjPStr`		RETURN	regular expression

From EMBOSS 1.0.0

Function embPatPrositeToRegExpEnds

Convert a prosite pattern to a regular expression string.

Prototype

AjPStr embPatPrositeToRegExpEnds (
      const AjPStr s,
      AjBool start,
      AjBool end
);

Type Name Read/Write Description

const AjPStr s Input prosite pattern

AjBool start Input must match start

AjBool end Input must match end

AjPStr RETURN regular expression

Type	Name	Read/Write	Description
`const AjPStr`	`s`	Input	prosite pattern
`AjBool`	`start`	Input	must match start
`AjBool`	`end`	Input	must match end
`AjPStr`		RETURN	regular expression

From EMBOSS 2.9.0

Function embPatRestrictNew

Create a new restriction object

Prototype

EmbPPatRestrict embPatRestrictNew (
      void
);

Type Name Read/Write Description

EmbPPatRestrict RETURN the allocated object

Type	Name	Read/Write	Description
`EmbPPatRestrict`		RETURN	the allocated object

From EMBOSS 1.0.0

Function embPatRestrictDel

Delete a restriction object

Prototype

void embPatRestrictDel (
      EmbPPatRestrict* thys
);

Type Name Read/Write Description

EmbPPatRestrict* thys Delete restriction object

void RETURN

Type	Name	Read/Write	Description
`EmbPPatRestrict*`	`thys`	Delete	restriction object
`void`		RETURN

From EMBOSS 1.0.0

Function embPatRestrictReadEntry

Read next restriction enzyme from re file

Prototype

AjBool embPatRestrictReadEntry (
      EmbPPatRestrict re,
      AjPFile inf
);

Type Name Read/Write Description

EmbPPatRestrict re Output restriction object to fill

AjPFile inf Modify input file pointer

AjBool RETURN True if read successful

Type	Name	Read/Write	Description
`EmbPPatRestrict`	`re`	Output	restriction object to fill
`AjPFile`	`inf`	Modify	input file pointer
`AjBool`		RETURN	True if read successful

From EMBOSS 1.0.0

Function embPatRestrictScan

Scan a sequence with a restriction object

Prototype

ajuint embPatRestrictScan (
      const EmbPPatRestrict enz,
      const AjPStr substr,
      const AjPStr binstr,
      const AjPStr revstr,
      const AjPStr binrev,
      ajuint len,
      AjBool ambiguity,
      AjBool plasmid,
      ajuint min,
      ajuint max,
      ajuint begin,
      AjPList l
);

Type Name Read/Write Description

const EmbPPatRestrict enz Input Enyme information

const AjPStr substr Input Sequence as ASCII

const AjPStr binstr Input Sequence as binary IUB

const AjPStr revstr Input Sequence as ASCII reversed

const AjPStr binrev Input Sequence as binary IUB reversed

ajuint len Input Length of sequence

AjBool ambiguity Input Allow ambiguity (binary search)

AjBool plasmid Input Allow circular DNA

ajuint min Input Minimum # of matches allowed

ajuint max Input Maximum # of matches

ajuint begin Input Sequence offset

AjPList l Modify List to push hits to

ajuint RETURN Number of matches

Type	Name	Read/Write	Description
`const EmbPPatRestrict`	`enz`	Input	Enyme information
`const AjPStr`	`substr`	Input	Sequence as ASCII
`const AjPStr`	`binstr`	Input	Sequence as binary IUB
`const AjPStr`	`revstr`	Input	Sequence as ASCII reversed
`const AjPStr`	`binrev`	Input	Sequence as binary IUB reversed
`ajuint`	`len`	Input	Length of sequence
`AjBool`	`ambiguity`	Input	Allow ambiguity (binary search)
`AjBool`	`plasmid`	Input	Allow circular DNA
`ajuint`	`min`	Input	Minimum # of matches allowed
`ajuint`	`max`	Input	Maximum # of matches
`ajuint`	`begin`	Input	Sequence offset
`AjPList`	`l`	Modify	List to push hits to
`ajuint`		RETURN	Number of matches

From EMBOSS 1.0.0

Function embPatKMPInit

Initialise a Knuth-Morris-Pratt pattern.

Prototype

void embPatKMPInit (
      const AjPStr pat,
      ajuint len,
      ajint* next
);

Type Name Read/Write Description

const AjPStr pat Input pattern

ajuint len Input length of pattern

ajint* next Output offset table

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint`	`len`	Input	length of pattern
`ajint*`	`next`	Output	offset table
`void`		RETURN

From EMBOSS 1.0.0

Function embPatKMPSearch

Perform a Knuth-Morris-Pratt search

Prototype

ajuint embPatKMPSearch (
      const AjPStr str,
      const AjPStr pat,
      ajuint slen,
      ajuint plen,
      const ajint* next,
      ajuint start
);

Type	Name	Read/Write	Description
`const AjPStr`	`str`	Input	string to search
`const AjPStr`	`pat`	Input	pattern to use
`ajuint`	`slen`	Input	length of string
`ajuint`	`plen`	Input	length of pattern
`const ajint*`	`next`	Input	array from embPatKMPInit (can be -1)
`ajuint`	`start`	Input	position within str to start search
`ajuint`		RETURN	Index of match in str or -1 if not found

From EMBOSS 1.0.0

Function embPatBMHInit

Initialise a Boyer-Moore-Horspool pattern.

Prototype

void embPatBMHInit (
      const AjPStr pat,
      ajuint len,
      ajint* skip
);

Type Name Read/Write Description

const AjPStr pat Input pattern

ajuint len Input pattern length

ajint* skip Output offset table (can be -1)

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint`	`len`	Input	pattern length
`ajint*`	`skip`	Output	offset table (can be -1)
`void`		RETURN

From EMBOSS 1.0.0

Function embPatBMHSearch

Perform a Boyer-Moore-Horspool search

Prototype

ajuint embPatBMHSearch (
      const AjPStr str,
      const AjPStr pat,
      ajuint slen,
      ajuint plen,
      const ajint* skip,
      ajuint start,
      AjBool left,
      AjBool right,
      AjPList l,
      const AjPStr name,
      ajuint begin
);

Type Name Read/Write Description

const AjPStr str Input string to search

const AjPStr pat Input pattern to use

ajuint slen Input length of string

ajuint plen Input length of pattern

const ajint* skip Input array from embPatBMHInit (can be -1)

ajuint start Input position within str to start search

AjBool left Input has to match the start

AjBool right Input has to match the end

AjPList l Modify list to push to

const AjPStr name Input name of entry

ajuint begin Input offset in orig sequence

ajuint RETURN number of hits

Type	Name	Read/Write	Description
`const AjPStr`	`str`	Input	string to search
`const AjPStr`	`pat`	Input	pattern to use
`ajuint`	`slen`	Input	length of string
`ajuint`	`plen`	Input	length of pattern
`const ajint*`	`skip`	Input	array from embPatBMHInit (can be -1)
`ajuint`	`start`	Input	position within str to start search
`AjBool`	`left`	Input	has to match the start
`AjBool`	`right`	Input	has to match the end
`AjPList`	`l`	Modify	list to push to
`const AjPStr`	`name`	Input	name of entry
`ajuint`	`begin`	Input	offset in orig sequence
`ajuint`		RETURN	number of hits

From EMBOSS 1.0.0

Function embPatBYPInit

Initialise a Baeza-Yates,Perleberg pattern.

Prototype

void embPatBYPInit (
      const AjPStr pat,
      ajuint len,
      EmbPPatBYPNode offset,
      ajint* buf
);

Type Name Read/Write Description

const AjPStr pat Input pattern

ajuint len Input pattern length

EmbPPatBYPNode offset Output character index

ajint* buf Output mismatch count

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint`	`len`	Input	pattern length
`EmbPPatBYPNode`	`offset`	Output	character index
`ajint*`	`buf`	Output	mismatch count
`void`		RETURN

From EMBOSS 1.0.0

Function embPatPushHit

Put a matching string search hit on the heap as an EmbPMatMatch structure

Prototype

void embPatPushHit (
      AjPList l,
      const AjPStr name,
      ajuint pos,
      ajuint plen,
      ajuint begin,
      ajuint mm
);

Type Name Read/Write Description

AjPList l Modify list to push to

const AjPStr name Input string name

ajuint pos Input Sequence match position

ajuint plen Input pattern length

ajuint begin Input Sequence offset

ajuint mm Input number of mismatches

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`l`	Modify	list to push to
`const AjPStr`	`name`	Input	string name
`ajuint`	`pos`	Input	Sequence match position
`ajuint`	`plen`	Input	pattern length
`ajuint`	`begin`	Input	Sequence offset
`ajuint`	`mm`	Input	number of mismatches
`void`		RETURN

From EMBOSS 1.0.0

Function embPatBYPSearch

Perform a Baeza-Yates,Perleberg search.

Prototype

ajuint embPatBYPSearch (
      const AjPStr str,
      const AjPStr name,
      ajuint begin,
      ajuint slen,
      ajuint plen,
      ajuint mm,
      EmbPPatBYPNode offset,
      ajint* buf,
      AjPList l,
      AjBool amino,
      AjBool carboxyl,
      const AjPStr pat
);

Type Name Read/Write Description

const AjPStr str Input search string

const AjPStr name Input search string

ajuint begin Input sequence offset

ajuint slen Input string length

ajuint plen Input pattern length

ajuint mm Input allowed mismatches (Hamming distance)

EmbPPatBYPNode offset Modify character index

ajint* buf Modify mismatch count array

AjPList l Modify list to push hits to

AjBool amino Input if true, match at amino terminal end

AjBool carboxyl Input if true, match at carboxyl terminal end

const AjPStr pat Input original pattern

ajuint RETURN number of matches

Type	Name	Read/Write	Description
`const AjPStr`	`str`	Input	search string
`const AjPStr`	`name`	Input	search string
`ajuint`	`begin`	Input	sequence offset
`ajuint`	`slen`	Input	string length
`ajuint`	`plen`	Input	pattern length
`ajuint`	`mm`	Input	allowed mismatches (Hamming distance)
`EmbPPatBYPNode`	`offset`	Modify	character index
`ajint*`	`buf`	Modify	mismatch count array
`AjPList`	`l`	Modify	list to push hits to
`AjBool`	`amino`	Input	if true, match at amino terminal end
`AjBool`	`carboxyl`	Input	if true, match at carboxyl terminal end
`const AjPStr`	`pat`	Input	original pattern
`ajuint`		RETURN	number of matches

From EMBOSS 1.0.0

Function embPatClassify

Classify patterns according to type. The pattern is set up upper case, has start and end processing turned into boolean flags. Sets other boolean flags for properties of the pattern so that a suitable processing method can be selected.

Prototype

AjBool embPatClassify (
      const AjPStr pat,
      AjPStr* cleanpat,
      AjBool* amino,
      AjBool* carboxyl,
      AjBool* fclass,
      AjBool* ajcompl,
      AjBool* dontcare,
      AjBool* range,
      AjBool protein
);

Type Name Read/Write Description

const AjPStr pat Input original pattern

AjPStr* cleanpat Output cleaned pattern

AjBool* amino Output set if must match start of sequence

AjBool* carboxyl Output set if must match end of sequence

AjBool* fclass Output set if class e.g. [ABC]

AjBool* ajcompl Output set if complement e.g.

AjBool* dontcare Output set if X (protein) or N (DNA)

AjBool* range Output set if range specified e.g. (3,10)

AjBool protein Input true if protein false if DNA

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	original pattern
`AjPStr*`	`cleanpat`	Output	cleaned pattern
`AjBool*`	`amino`	Output	set if must match start of sequence
`AjBool*`	`carboxyl`	Output	set if must match end of sequence
`AjBool*`	`fclass`	Output	set if class e.g. [ABC]
`AjBool*`	`ajcompl`	Output	set if complement e.g.
`AjBool*`	`dontcare`	Output	set if X (protein) or N (DNA)
`AjBool*`	`range`	Output	set if range specified e.g. (3,10)
`AjBool`	`protein`	Input	true if protein false if DNA
`AjBool`		RETURN	ajTrue on success

Usage

ajcompl: ABC From EMBOSS 1.0.0

Function embPatSOInit

Initialise a Shift-Or pattern.

Prototype

void embPatSOInit (
      const AjPStr pat,
      ajuint* table,
      ajuint* limit
);

Type Name Read/Write Description

const AjPStr pat Input pattern

ajuint* table Output SO table

ajuint* limit Output match limit

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint*`	`table`	Output	SO table
`ajuint*`	`limit`	Output	match limit
`void`		RETURN

From EMBOSS 1.0.0

Function embPatSOSearch

Perform a Shift-OR search.

Prototype

ajuint embPatSOSearch (
      const AjPStr str,
      const AjPStr name,
      ajint first,
      ajuint begin,
      ajuint plen,
      const ajuint* table,
      ajuint limit,
      AjPList l,
      AjBool amino,
      AjBool carboxyl
);

Type Name Read/Write Description

const AjPStr str Input search string

const AjPStr name Input search string

ajint first Input first character of pattern (as an integer)

ajuint begin Input sequence offset

ajuint plen Input pattern length

const ajuint* table Input SO table

ajuint limit Input SO limit

AjPList l Modify list to push hits to

AjBool amino Input must match start

AjBool carboxyl Input must match end

ajuint RETURN number of matches

Type	Name	Read/Write	Description
`const AjPStr`	`str`	Input	search string
`const AjPStr`	`name`	Input	search string
`ajint`	`first`	Input	first character of pattern (as an integer)
`ajuint`	`begin`	Input	sequence offset
`ajuint`	`plen`	Input	pattern length
`const ajuint*`	`table`	Input	SO table
`ajuint`	`limit`	Input	SO limit
`AjPList`	`l`	Modify	list to push hits to
`AjBool`	`amino`	Input	must match start
`AjBool`	`carboxyl`	Input	must match end
`ajuint`		RETURN	number of matches

From EMBOSS 1.0.0

Function embPatBYGCInit

Initialise a Baeza-Yates Gonnet class pattern.

Prototype

void embPatBYGCInit (
      const AjPStr pat,
      ajuint* m,
      ajuint* table,
      ajuint* limit
);

Type Name Read/Write Description

const AjPStr pat Input pattern

ajuint* m Output real pattern length

ajuint* table Output SO table

ajuint* limit Output match limit

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint*`	`m`	Output	real pattern length
`ajuint*`	`table`	Output	SO table
`ajuint*`	`limit`	Output	match limit
`void`		RETURN

From EMBOSS 1.0.0

Function embPatBYGSearch

Perform a Baeza-Yates Gonnet search.

Prototype

ajuint embPatBYGSearch (
      const AjPStr str,
      const AjPStr name,
      ajuint begin,
      ajuint plen,
      const ajuint* table,
      ajuint limit,
      AjPList l,
      AjBool amino,
      AjBool carboxyl
);

Type Name Read/Write Description

const AjPStr str Input search string

const AjPStr name Input search string

ajuint begin Input sequence offset

ajuint plen Input pattern length

const ajuint* table Input SO table

ajuint limit Input SO limit

AjPList l Modify list to push hits to

AjBool amino Input must match start

AjBool carboxyl Input must match end

ajuint RETURN number of matches

Type	Name	Read/Write	Description
`const AjPStr`	`str`	Input	search string
`const AjPStr`	`name`	Input	search string
`ajuint`	`begin`	Input	sequence offset
`ajuint`	`plen`	Input	pattern length
`const ajuint*`	`table`	Input	SO table
`ajuint`	`limit`	Input	SO limit
`AjPList`	`l`	Modify	list to push hits to
`AjBool`	`amino`	Input	must match start
`AjBool`	`carboxyl`	Input	must match end
`ajuint`		RETURN	number of matches

From EMBOSS 1.0.0

Function embPatTUInit

Initialise a Tarhio-Ukkonen search

Prototype

void embPatTUInit (
      const AjPStr pat,
      ajuint** skipm,
      ajuint m,
      ajuint k
);

Type Name Read/Write Description

const AjPStr pat Input pattern

ajuint** skipm Output mismatch skip array

ajuint m Input real pattern length

ajuint k Input allowed mismatches

void RETURN

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint**`	`skipm`	Output	mismatch skip array
`ajuint`	`m`	Input	real pattern length
`ajuint`	`k`	Input	allowed mismatches
`void`		RETURN

From EMBOSS 1.0.0

Function embPatTUSearch

Perform a Tarhio-Ukkonen search

Prototype

ajuint embPatTUSearch (
      const AjPStr pat,
      const AjPStr text,
      ajuint slen,
      ajuint* const* skipm,
      ajuint m,
      ajuint k,
      ajuint begin,
      AjPList l,
      AjBool amino,
      AjBool carboxyl,
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr pat Input pattern

const AjPStr text Input text to search (incl ajcompl/class)

ajuint slen Input length of text

ajuint* const* skipm Input mismatch skip array

ajuint m Input real pattern length

ajuint k Input allowed mismatches

ajuint begin Input text offset

AjPList l Modify list to push to

AjBool amino Input true if text start

AjBool carboxyl Input true if text end

const AjPStr name Input name of text

ajuint RETURN number of hits

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`const AjPStr`	`text`	Input	text to search (incl ajcompl/class)
`ajuint`	`slen`	Input	length of text
`ajuint* const*`	`skipm`	Input	mismatch skip array
`ajuint`	`m`	Input	real pattern length
`ajuint`	`k`	Input	allowed mismatches
`ajuint`	`begin`	Input	text offset
`AjPList`	`l`	Modify	list to push to
`AjBool`	`amino`	Input	true if text start
`AjBool`	`carboxyl`	Input	true if text end
`const AjPStr`	`name`	Input	name of text
`ajuint`		RETURN	number of hits

From EMBOSS 1.0.0

Function embPatTUBInit

Initialise a Tarhio-Ukkonen-Bleasby search

Prototype

void embPatTUBInit (
      const AjPStr pat,
      ajuint** skipm,
      ajuint m,
      ajuint k,
      ajuint plen
);

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`ajuint**`	`skipm`	Output	mismatch skip array
`ajuint`	`m`	Input	real pattern length
`ajuint`	`k`	Input	allowed mismatches
`ajuint`	`plen`	Input	full pattern length (incl ajcompl & class)
`void`		RETURN

From EMBOSS 1.0.0

Function embPatTUBSearch

Perform a Tarhio-Ukkonen-Bleasby search

Prototype

ajuint embPatTUBSearch (
      const AjPStr pat,
      const AjPStr text,
      ajuint slen,
      ajuint* const* skipm,
      ajuint m,
      ajuint k,
      ajuint begin,
      AjPList l,
      AjBool amino,
      AjBool carboxyl,
      const AjPStr name,
      ajuint plen
);

Type	Name	Read/Write	Description
`const AjPStr`	`pat`	Input	pattern
`const AjPStr`	`text`	Input	text to search (incl ajcompl/class)
`ajuint`	`slen`	Input	length of text
`ajuint* const*`	`skipm`	Input	mismatch skip array
`ajuint`	`m`	Input	real pattern length
`ajuint`	`k`	Input	allowed mismatches
`ajuint`	`begin`	Input	text offset
`AjPList`	`l`	Modify	list to push to
`AjBool`	`amino`	Input	true if text start
`AjBool`	`carboxyl`	Input	true if text end
`const AjPStr`	`name`	Input	name of text
`ajuint`	`plen`	Input	total pattern length
`ajuint`		RETURN	number of hits

From EMBOSS 1.0.0

Function embPatBruteForce

Match pattern to a sequence

Prototype

ajuint embPatBruteForce (
      const AjPStr seq,
      const AjPStr pat,
      AjBool amino,
      AjBool carboxyl,
      AjPList l,
      ajuint begin,
      ajuint mm,
      const AjPStr name
);

Type Name Read/Write Description

const AjPStr seq Input text

const AjPStr pat Input pattern

AjBool amino Input true if must match start

AjBool carboxyl Input true if must match end

AjPList l Modify list on which to push hits

ajuint begin Input text offset

ajuint mm Input allowed mismatches

const AjPStr name Input text entry name

ajuint RETURN number of hits

Type	Name	Read/Write	Description
`const AjPStr`	`seq`	Input	text
`const AjPStr`	`pat`	Input	pattern
`AjBool`	`amino`	Input	true if must match start
`AjBool`	`carboxyl`	Input	true if must match end
`AjPList`	`l`	Modify	list on which to push hits
`ajuint`	`begin`	Input	text offset
`ajuint`	`mm`	Input	allowed mismatches
`const AjPStr`	`name`	Input	text entry name
`ajuint`		RETURN	number of hits

From EMBOSS 1.0.0

Function embPatVariablePattern

Match variable pattern against constant text. Used for matching many patterns against one sequence.

Prototype

ajuint embPatVariablePattern (
      const AjPStr pattern,
      const AjPStr text,
      const AjPStr patname,
      AjPList l,
      ajuint mode,
      ajuint mismatch,
      ajuint begin
);

Type Name Read/Write Description

const AjPStr pattern Input pattern to match

const AjPStr text Input text to scan

const AjPStr patname Input ID or AC of pattern

AjPList l Modify list on which to push hits

ajuint mode Input 1 for protein, 0 for nucleic acid

ajuint mismatch Input allowed mismatches

ajuint begin Input text offset

ajuint RETURN number of hits

Type	Name	Read/Write	Description
`const AjPStr`	`pattern`	Input	pattern to match
`const AjPStr`	`text`	Input	text to scan
`const AjPStr`	`patname`	Input	ID or AC of pattern
`AjPList`	`l`	Modify	list on which to push hits
`ajuint`	`mode`	Input	1 for protein, 0 for nucleic acid
`ajuint`	`mismatch`	Input	allowed mismatches
`ajuint`	`begin`	Input	text offset
`ajuint`		RETURN	number of hits

From EMBOSS 1.0.0

Function embPatRestrictPreferred

Replace RE names by the name of the prototype for that RE

Prototype

void embPatRestrictPreferred (
      AjPList l,
      const AjPTable t
);

Type Name Read/Write Description

AjPList l Modify list of EmbPMatMatch hits

const AjPTable t Input table from embossre.equ file

void RETURN

Type	Name	Read/Write	Description
`AjPList`	`l`	Modify	list of EmbPMatMatch hits
`const AjPTable`	`t`	Input	table from embossre.equ file
`void`		RETURN

From EMBOSS 2.7.0

Function embPatRestrictRestrict

Cut down the number of restriction enzyme hits from embPatRestrictScan Notably double reporting of symmetric palindromes and reporting of isoschizomers. Also provides an optional alphabetic sort.

Prototype

ajuint embPatRestrictRestrict (
      AjPList l,
      ajuint hits,
      AjBool isos,
      AjBool alpha
);

Type Name Read/Write Description

AjPList l Modify list of hits from embPatRestrictScan

ajuint hits Input number of hits from embPatRestrictScan

AjBool isos Input Allow isoschizomers

AjBool alpha Input Sort alphabetically

ajuint RETURN adjusted number of hits

Type	Name	Read/Write	Description
`AjPList`	`l`	Modify	list of hits from embPatRestrictScan
`ajuint`	`hits`	Input	number of hits from embPatRestrictScan
`AjBool`	`isos`	Input	Allow isoschizomers
`AjBool`	`alpha`	Input	Sort alphabetically
`ajuint`		RETURN	adjusted number of hits

From EMBOSS 1.0.0

Function embPatRestrictStartCompare

Sort restriction site hits on the basis of start position

Prototype

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

Type Name Read/Write Description

const void* a Input First EmbPMatMatch hit

const void* b Input Second EmbPMatMatch hit

ajint RETURN 0 if a and b are equal -ve if a is less than b, +ve if a is greater than b

Type	Name	Read/Write	Description
`const void*`	`a`	Input	First EmbPMatMatch hit
`const void*`	`b`	Input	Second EmbPMatMatch hit
`ajint`		RETURN	0 if a and b are equal -ve if a is less than b, +ve if a is greater than b

From EMBOSS 1.13.0

Function embPatRestrictCutCompare

Sort restriction site hits on the basis of cut position

Prototype

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

Type	Name	Read/Write	Description
`const void*`	`a`	Input	First EmbPMatMatch hit
`const void*`	`b`	Input	Second EmbPMatMatch hit
`ajint`		RETURN	0 if a and b are equal -ve if a is less than b, +ve if a is greater than b

From EMBOSS 1.13.0

Function embPatRestrictNameCompare

Sort restriction site hits on the basis of enzyme name

Prototype

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

Type	Name	Read/Write	Description
`const void*`	`a`	Input	First EmbPMatMatch hit
`const void*`	`b`	Input	Second EmbPMatMatch hit
`ajint`		RETURN	0 if a and b are equal -ve if a is less than b, +ve if a is greater than b

From EMBOSS 1.13.0

Function embPatRestrictMatch

Main Restriction function. Scans sequence and rejects unwanted cutters

Prototype

ajuint embPatRestrictMatch (
      const AjPSeq seq,
      ajuint begin,
      ajuint end,
      AjPFile enzfile,
      AjPFile methfile,
      const AjPStr enzymes,
      ajuint sitelen,
      AjBool plasmid,
      AjBool ambiguity,
      ajuint min,
      ajuint max,
      AjBool blunt,
      AjBool sticky,
      AjBool commercial,
      AjBool methyl,
      AjPList l
);

Type Name Read/Write Description

const AjPSeq seq Input sequence

ajuint begin Input start position in sequence

ajuint end Input end position in sequence

AjPFile enzfile Modify file pointer to .enz file

AjPFile methfile Modify file pointer to methylation data file

const AjPStr enzymes Input comma separated list of REs or NULL for all

ajuint sitelen Input minimum length of recognition site

AjBool plasmid Input Circular DNA

AjBool ambiguity Input Allow ambiguities

ajuint min Input minimum number of true cuts

ajuint max Input maximum number of true cuts

AjBool blunt Input Allow blunt cutters

AjBool sticky Input Allow sticky cutters

AjBool commercial Input Allow Only report REs with a supplier

AjBool methyl Input Mark methylated bases as 'N'

AjPList l Modify list for (EmbPMatMatch) hits

ajuint RETURN number of hits

Type	Name	Read/Write	Description
`const AjPSeq`	`seq`	Input	sequence
`ajuint`	`begin`	Input	start position in sequence
`ajuint`	`end`	Input	end position in sequence
`AjPFile`	`enzfile`	Modify	file pointer to .enz file
`AjPFile`	`methfile`	Modify	file pointer to methylation data file
`const AjPStr`	`enzymes`	Input	comma separated list of REs or NULL for all
`ajuint`	`sitelen`	Input	minimum length of recognition site
`AjBool`	`plasmid`	Input	Circular DNA
`AjBool`	`ambiguity`	Input	Allow ambiguities
`ajuint`	`min`	Input	minimum number of true cuts
`ajuint`	`max`	Input	maximum number of true cuts
`AjBool`	`blunt`	Input	Allow blunt cutters
`AjBool`	`sticky`	Input	Allow sticky cutters
`AjBool`	`commercial`	Input	Allow Only report REs with a supplier
`AjBool`	`methyl`	Input	Mark methylated bases as 'N'
`AjPList`	`l`	Modify	list for (EmbPMatMatch) hits
`ajuint`		RETURN	number of hits

From EMBOSS 1.0.0

Function embPatGetType

Return the type of a pattern

Prototype

ajuint embPatGetType (
      const AjPStr pattern,
      AjPStr* cleanpat,
      ajuint mismatch,
      AjBool protein,
      ajuint* m,
      AjBool* left,
      AjBool* right
);

Type Name Read/Write Description

const AjPStr pattern Input original pattern

AjPStr* cleanpat Output cleaned pattern

ajuint mismatch Input number of allowed mismatches

AjBool protein Input true if protein

ajuint* m Output real length of pattern

AjBool* left Output must match left begin

AjBool* right Output must match right

ajuint RETURN type of pattern

Type	Name	Read/Write	Description
`const AjPStr`	`pattern`	Input	original pattern
`AjPStr*`	`cleanpat`	Output	cleaned pattern
`ajuint`	`mismatch`	Input	number of allowed mismatches
`AjBool`	`protein`	Input	true if protein
`ajuint*`	`m`	Output	real length of pattern
`AjBool*`	`left`	Output	must match left begin
`AjBool*`	`right`	Output	must match right
`ajuint`		RETURN	type of pattern

From EMBOSS 1.0.0

Function embPatCompile

Compile a pattern classified by embPatGetType

Prototype

void embPatCompile (
      ajuint type,
      const AjPStr pattern,
      ajuint* plen,
      ajint** buf,
      EmbPPatBYPNode off,
      ajuint** sotable,
      ajuint* solimit,
      ajuint* m,
      AjPStr* regexp,
      ajuint*** skipm,
      ajuint mismatch
);

Type Name Read/Write Description

ajuint type Input pattern type

const AjPStr pattern Input original pattern

ajuint* plen Output pattern length

ajint** buf Output buffer for BMH and BYP search (can be -1)

EmbPPatBYPNode off Output offset buffer for B-Y/P search

ajuint** sotable Output buffer for SHIFT-OR

ajuint* solimit Output limit for SHIFT-OR

ajuint* m Output real length of pattern (from embPatGetType)

AjPStr* regexp Output PCRE regexp string

ajuint*** skipm Output skip buffer for Tarhio-Ukkonen

ajuint mismatch Input number of allowed mismatches

void RETURN

Type	Name	Read/Write	Description
`ajuint`	`type`	Input	pattern type
`const AjPStr`	`pattern`	Input	original pattern
`ajuint*`	`plen`	Output	pattern length
`ajint**`	`buf`	Output	buffer for BMH and BYP search (can be -1)
`EmbPPatBYPNode`	`off`	Output	offset buffer for B-Y/P search
`ajuint**`	`sotable`	Output	buffer for SHIFT-OR
`ajuint*`	`solimit`	Output	limit for SHIFT-OR
`ajuint*`	`m`	Output	real length of pattern (from embPatGetType)
`AjPStr*`	`regexp`	Output	PCRE regexp string
`ajuint***`	`skipm`	Output	skip buffer for Tarhio-Ukkonen
`ajuint`	`mismatch`	Input	number of allowed mismatches
`void`		RETURN

From EMBOSS 1.0.0

Function embPatFuzzSearch

Fuzzy search after embPatGetType and embPatCompile

Prototype

void embPatFuzzSearch (
      ajuint type,
      ajuint begin,
      const AjPStr pattern,
      const AjPStr name,
      const AjPStr text,
      AjPList l,
      ajuint plen,
      ajuint mismatch,
      AjBool left,
      AjBool right,
      ajint* buf,
      EmbPPatBYPNode off,
      const ajuint* sotable,
      ajuint solimit,
      const AjPStr regexp,
      ajuint* const* skipm,
      ajuint* hits,
      ajuint m,
      const void** tidy
);

Type Name Read/Write Description

ajuint type Input pattern type

ajuint begin Input text displacement (1=start)

const AjPStr pattern Input processed pattern

const AjPStr name Input name associated with text

const AjPStr text Input text

AjPList l Modify list to push hits onto

ajuint plen Input pattern length

ajuint mismatch Input number of allowed mismatches

AjBool left Input must match left

AjBool right Input must match right

ajint* buf Modify buffer for BMH search

EmbPPatBYPNode off Modify offset buffer for B-Y/P search

const ajuint* sotable Input buffer for SHIFT-OR

ajuint solimit Input limit for SHIFT-OR

const AjPStr regexp Input PCRE regexp string

ajuint* const* skipm Input skip buffer for Tarhio-Ukkonen-Bleasby

ajuint* hits Output number of hits

ajuint m Input real pat length (from embPatGetType/embPatCompile)

const void** tidy Output data to free

void RETURN

Type	Name	Read/Write	Description
`ajuint`	`type`	Input	pattern type
`ajuint`	`begin`	Input	text displacement (1=start)
`const AjPStr`	`pattern`	Input	processed pattern
`const AjPStr`	`name`	Input	name associated with text
`const AjPStr`	`text`	Input	text
`AjPList`	`l`	Modify	list to push hits onto
`ajuint`	`plen`	Input	pattern length
`ajuint`	`mismatch`	Input	number of allowed mismatches
`AjBool`	`left`	Input	must match left
`AjBool`	`right`	Input	must match right
`ajint*`	`buf`	Modify	buffer for BMH search
`EmbPPatBYPNode`	`off`	Modify	offset buffer for B-Y/P search
`const ajuint*`	`sotable`	Input	buffer for SHIFT-OR
`ajuint`	`solimit`	Input	limit for SHIFT-OR
`const AjPStr`	`regexp`	Input	PCRE regexp string
`ajuint* const*`	`skipm`	Input	skip buffer for Tarhio-Ukkonen-Bleasby
`ajuint*`	`hits`	Output	number of hits
`ajuint`	`m`	Input	real pat length (from embPatGetType/embPatCompile)
`const void**`	`tidy`	Output	data to free
`void`		RETURN

From EMBOSS 1.0.0

Function embPatCompileII

Compile a pattern classified by embPatGetType

Prototype

void embPatCompileII (
      AjPPatComp thys,
      ajuint mismatch
);

Type Name Read/Write Description

AjPPatComp thys Modify Prosite pattern stucture

ajuint mismatch Input number of allowed mismatches

void RETURN

Type	Name	Read/Write	Description
`AjPPatComp`	`thys`	Modify	Prosite pattern stucture
`ajuint`	`mismatch`	Input	number of allowed mismatches
`void`		RETURN

From EMBOSS 4.0.0

Function embPatFuzzSearchII

Fuzzy search after embPatGetType and embPatCompile

Prototype

void embPatFuzzSearchII (
      AjPPatComp thys,
      ajuint begin,
      const AjPStr name,
      const AjPStr text,
      AjPList l,
      ajuint mismatch,
      ajuint* hits,
      const void** tidy
);

Type Name Read/Write Description

AjPPatComp thys Modify Prosite pattern stucture

ajuint begin Input Sequence displacement (1=start)

const AjPStr name Input Name associated with sequence

const AjPStr text Input Sequence

AjPList l Modify List to push hits onto

ajuint mismatch Input number of allowed mismatches

ajuint* hits Output number of hits

const void** tidy Output data to free

void RETURN

Type	Name	Read/Write	Description
`AjPPatComp`	`thys`	Modify	Prosite pattern stucture
`ajuint`	`begin`	Input	Sequence displacement (1=start)
`const AjPStr`	`name`	Input	Name associated with sequence
`const AjPStr`	`text`	Input	Sequence
`AjPList`	`l`	Modify	List to push hits onto
`ajuint`	`mismatch`	Input	number of allowed mismatches
`ajuint*`	`hits`	Output	number of hits
`const void**`	`tidy`	Output	data to free
`void`		RETURN

From EMBOSS 4.0.0

Function embPatGetTypeII

Return the type of a pattern

Prototype

ajuint embPatGetTypeII (
      AjPPatComp thys,
      const AjPStr pattern,
      ajuint mismatch,
      AjBool protein
);

Type Name Read/Write Description

AjPPatComp thys Modify Prosite pattern stucture

const AjPStr pattern Input Original pattern

ajuint mismatch Input Number of allowed mismatches

AjBool protein Input True if protein

ajuint RETURN type of pattern

Type	Name	Read/Write	Description
`AjPPatComp`	`thys`	Modify	Prosite pattern stucture
`const AjPStr`	`pattern`	Input	Original pattern
`ajuint`	`mismatch`	Input	Number of allowed mismatches
`AjBool`	`protein`	Input	True if protein
`ajuint`		RETURN	type of pattern

From EMBOSS 4.0.0