embpat.c

Function embPatSeqCreateRegExp

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

Synopsis

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.

Input

thys:	(Input)	string to create reg expr from.
protein:	(Input)	is it a protein.

Returns

AjPStr:

the new regular expression.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatSeqCreateRegExpC

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

Synopsis

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.

Input

ptr:	(Input)	text to create reg expr from.
protein:	(Input)	is it a protein.

Returns

AjPStr:

the new regular expression.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatSeqMatchFind

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

Synopsis

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.

Input

seq:	(Input)	Sequence to be searched.
reg:	(Input)	regular expression string.

Returns

EmbPPatMatch:

Results of the pattern matching.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatSeqMatchFindC

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

Synopsis

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.

Input

seq:	(Input)	Sequence to be searched.
reg:	(Input)	regular expression text.

Returns

EmbPPatMatch:

Results of the pattern matching.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchFind

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

Synopsis

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.

Input

regexp:	(Input)	Regular expression string.
strng:	(Input)	String to be searched.
left:	(Input)	has to match the start
right:	(Input)	has to match the end

Returns

EmbPPatMatch:

Results of the pattern matching.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchFindC

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

Synopsis

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.

Input

regexp:	(Input)	Regular expression string.
sptr:	(Input)	String to be searched.
left:	(Input)	has to match the start
right:	(Input)	has to match the end

Returns

EmbPPatMatch:

Results of the pattern matching.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchGetLen

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

Synopsis

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.

Input

data:	(Input)	results of match.
indexnum:	(Input)	index to structure.

Returns

ajuint:

returns -1 if not available.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchGetEnd

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

Synopsis

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.

Input

data:	(Input)	results of match.
indexnum:	(Input)	index to structure.

Returns

ajuint:

returns -1 if not available.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchGetNumber

Returns the number of pattern matches in the structure.

Synopsis

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.

Input

data:

(Input)

results of match.

Returns

ajuint:

returns -1 if not available.

Description

Returns the number of pattern matches in the structure.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchGetStart

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

Synopsis

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.

Input

data:	(Input)	results of match.
indexnum:	(Input)	index to structure.

Returns

ajuint:

returns -1 if not available.

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatMatchDel

Free all the memory from the pattern match search.

Synopsis

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

Output

pthis:

(Delete)

results to be freed.

Returns

void:

No return value

Description

Free all the memory from the pattern match search.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatPrositeToRegExp

Convert a prosite pattern to a regular expression

Start and end are indicated by boolean options, as the pattern may have been processed for the other pattern matching methods

Synopsis

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

Input

(Input)

prosite pattern

Returns

AjPStr:

regular expression

Description

Convert a prosite pattern to a regular expression

Start and end are indicated by boolean options, as the pattern may have been processed for the other pattern matching methods

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatPrositeToRegExpEnds

Convert a prosite pattern to a regular expression string.

start and end say whether the ends should match in case this is a processed pattern, but there is still a check for angle brackets.

Synopsis

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

Input

s:	(Input)	prosite pattern
start:	(Input)	must match start
end:	(Input)	must match end

Returns

AjPStr:

regular expression

Description

Convert a prosite pattern to a regular expression string.

start and end say whether the ends should match in case this is a processed pattern, but there is still a check for angle brackets.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictNew

Create a new restriction object

Synopsis

Prototype

EmbPPatRestrict embPatRestrictNew (
      void
);

Type Name Read/Write Description

EmbPPatRestrict RETURN the allocated object

Type	Name	Read/Write	Description
EmbPPatRestrict		RETURN	the allocated object

Returns

EmbPPatRestrict:

the allocated object

Description

Create a new restriction object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictDel

Delete a restriction object

Synopsis

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

Output

thys:

(Delete)

restriction object

Returns

void:

No return value

Description

Delete a restriction object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictReadEntry

Read next restriction enzyme from re file

Synopsis

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

Output

re:

(Output)

restriction object to fill

Input & Output

inf:

(Modify)

input file pointer

Returns

AjBool:

True if read successful

Description

Read next restriction enzyme from re file

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictScan

Scan a sequence with a restriction object

Synopsis

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

Input

enz:	(Input)	Enyme information
substr:	(Input)	Sequence as ASCII
binstr:	(Input)	Sequence as binary IUB
revstr:	(Input)	Sequence as ASCII reversed
binrev:	(Input)	Sequence as binary IUB reversed
len:	(Input)	Length of sequence
ambiguity:	(Input)	Allow ambiguity (binary search)
plasmid:	(Input)	Allow circular DNA
min:	(Input)	Minimum # of matches allowed
max:	(Input)	Maximum # of matches
begin:	(Input)	Sequence offset

Input & Output

(Modify)

List to push hits to

Returns

ajuint:

Number of matches

Description

Scan a sequence with a restriction object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatKMPInit

Initialise a Knuth-Morris-Pratt pattern.

Synopsis

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

Input

pat:	(Input)	pattern
len:	(Input)	length of pattern

Output

next:

(Output)

offset table

Returns

void:

No return value

Description

Initialise a Knuth-Morris-Pratt pattern.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatKMPSearch

Perform a Knuth-Morris-Pratt search

Synopsis

Prototype

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

Input

str:	(Input)	string to search
pat:	(Input)	pattern to use
slen:	(Input)	length of string
plen:	(Input)	length of pattern
next:	(Input)	array from embPatKMPInit (can be -1)
start:	(Input)	position within str to start search

Returns

ajuint:

Index of match in str or -1 if not found

Description

Perform a Knuth-Morris-Pratt search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBMHInit

Initialise a Boyer-Moore-Horspool pattern.

Synopsis

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

Input

pat:	(Input)	pattern
len:	(Input)	pattern length

Output

skip:

(Output)

offset table (can be -1)

Returns

void:

No return value

Description

Initialise a Boyer-Moore-Horspool pattern.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBMHSearch

Perform a Boyer-Moore-Horspool search

Synopsis

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

Input

str:	(Input)	string to search
pat:	(Input)	pattern to use
slen:	(Input)	length of string
plen:	(Input)	length of pattern
skip:	(Input)	array from embPatBMHInit (can be -1)
start:	(Input)	position within str to start search
left:	(Input)	has to match the start
right:	(Input)	has to match the end
name:	(Input)	name of entry
begin:	(Input)	offset in orig sequence

Input & Output

(Modify)

list to push to

Returns

ajuint:

number of hits

Description

Perform a Boyer-Moore-Horspool search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBYPInit

Initialise a Baeza-Yates,Perleberg pattern.

Synopsis

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

Input

pat:	(Input)	pattern
len:	(Input)	pattern length

Output

offset:	(Output)	character index
buf:	(Output)	mismatch count

Returns

void:

No return value

Description

Initialise a Baeza-Yates,Perleberg pattern.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatPushHit

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

Synopsis

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

Input

name:	(Input)	string name
pos:	(Input)	Sequence match position
plen:	(Input)	pattern length
begin:	(Input)	Sequence offset
mm:	(Input)	number of mismatches

Input & Output

(Modify)

list to push to

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBYPSearch

Perform a Baeza-Yates,Perleberg search.

Synopsis

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

Input

str:	(Input)	search string
name:	(Input)	search string
begin:	(Input)	sequence offset
slen:	(Input)	string length
plen:	(Input)	pattern length
mm:	(Input)	allowed mismatches (Hamming distance)
amino:	(Input)	if true, match at amino terminal end
carboxyl:	(Input)	if true, match at carboxyl terminal end
pat:	(Input)	original pattern

Input & Output

offset:	(Modify)	character index
buf:	(Modify)	mismatch count array
l:	(Modify)	list to push hits to

Returns

ajuint:

number of matches

Description

Perform a Baeza-Yates,Perleberg search.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

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.

Synopsis

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

Input

pat:	(Input)	original pattern
protein:	(Input)	true if protein false if DNA

Output

cleanpat:	(Output)	cleaned pattern
amino:	(Output)	set if must match start of sequence
carboxyl:	(Output)	set if must match end of sequence
fclass:	(Output)	set if class e.g. [ABC]
ajcompl:	(Output)	set if complement e.g.
dontcare:	(Output)	set if X (protein) or N (DNA)
range:	(Output)	set if range specified e.g. (3,10)

Returns

AjBool:

ajTrue on success

Description

Usage

ajcompl: ABC

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatSOInit

Initialise a Shift-Or pattern.

Synopsis

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

Input

pat:

(Input)

pattern

Output

table:	(Output)	SO table
limit:	(Output)	match limit

Returns

void:

No return value

Description

Initialise a Shift-Or pattern.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatSOSearch

Perform a Shift-OR search.

Synopsis

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

Input

str:	(Input)	search string
name:	(Input)	search string
first:	(Input)	first character of pattern (as an integer)
begin:	(Input)	sequence offset
plen:	(Input)	pattern length
table:	(Input)	SO table
limit:	(Input)	SO limit
amino:	(Input)	must match start
carboxyl:	(Input)	must match end

Input & Output

(Modify)

list to push hits to

Returns

ajuint:

number of matches

Description

Perform a Shift-OR search.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBYGCInit

Initialise a Baeza-Yates Gonnet class pattern.

Synopsis

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

Input

pat:

(Input)

pattern

Output

m:	(Output)	real pattern length
table:	(Output)	SO table
limit:	(Output)	match limit

Returns

void:

No return value

Description

Initialise a Baeza-Yates Gonnet class pattern.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBYGSearch

Perform a Baeza-Yates Gonnet search.

Synopsis

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

Input

str:	(Input)	search string
name:	(Input)	search string
begin:	(Input)	sequence offset
plen:	(Input)	pattern length
table:	(Input)	SO table
limit:	(Input)	SO limit
amino:	(Input)	must match start
carboxyl:	(Input)	must match end

Input & Output

(Modify)

list to push hits to

Returns

ajuint:

number of matches

Description

Perform a Baeza-Yates Gonnet search.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatTUInit

Initialise a Tarhio-Ukkonen search

Synopsis

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

Input

pat:	(Input)	pattern
m:	(Input)	real pattern length
k:	(Input)	allowed mismatches

Output

skipm:

(Output)

mismatch skip array

Returns

void:

No return value

Description

Initialise a Tarhio-Ukkonen search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatTUSearch

Perform a Tarhio-Ukkonen search

Synopsis

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

Input

pat:	(Input)	pattern
text:	(Input)	text to search (incl ajcompl/class)
slen:	(Input)	length of text
skipm:	(Input)	mismatch skip array
m:	(Input)	real pattern length
k:	(Input)	allowed mismatches
begin:	(Input)	text offset
amino:	(Input)	true if text start
carboxyl:	(Input)	true if text end
name:	(Input)	name of text

Input & Output

(Modify)

list to push to

Returns

ajuint:

number of hits

Description

Perform a Tarhio-Ukkonen search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatTUBInit

Initialise a Tarhio-Ukkonen-Bleasby search

Synopsis

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

Input

pat:	(Input)	pattern
m:	(Input)	real pattern length
k:	(Input)	allowed mismatches
plen:	(Input)	full pattern length (incl ajcompl & class)

Output

skipm:

(Output)

mismatch skip array

Returns

void:

No return value

Description

Initialise a Tarhio-Ukkonen-Bleasby search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatTUBSearch

Perform a Tarhio-Ukkonen-Bleasby search

Synopsis

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
);

Input

pat:	(Input)	pattern
text:	(Input)	text to search (incl ajcompl/class)
slen:	(Input)	length of text
skipm:	(Input)	mismatch skip array
m:	(Input)	real pattern length
k:	(Input)	allowed mismatches
begin:	(Input)	text offset
amino:	(Input)	true if text start
carboxyl:	(Input)	true if text end
name:	(Input)	name of text
plen:	(Input)	total pattern length

Input & Output

(Modify)

list to push to

Returns

ajuint:

number of hits

Description

Perform a Tarhio-Ukkonen-Bleasby search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatBruteForce

Match pattern to a sequence

Synopsis

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

Input

seq:	(Input)	text
pat:	(Input)	pattern
amino:	(Input)	true if must match start
carboxyl:	(Input)	true if must match end
begin:	(Input)	text offset
mm:	(Input)	allowed mismatches
name:	(Input)	text entry name

Input & Output

(Modify)

list on which to push hits

Returns

ajuint:

number of hits

Description

Match pattern to a sequence

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatVariablePattern

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

Synopsis

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

Input

pattern:	(Input)	pattern to match
text:	(Input)	text to scan
patname:	(Input)	ID or AC of pattern
mode:	(Input)	1 for protein, 0 for nucleic acid
mismatch:	(Input)	allowed mismatches
begin:	(Input)	text offset

Input & Output

(Modify)

list on which to push hits

Returns

ajuint:

number of hits

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictPreferred

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

Synopsis

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

Input

(Input)

table from embossre.equ file

Input & Output

(Modify)

list of EmbPMatMatch hits

Returns

void:

No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

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.

If we don't allow isoschizomers, then names of all isoschizomers found will be added to the string 'iso' in the returned list of EmbPMatMatch structures. If 'isos' is AjTrue then they will be left alone.

Synopsis

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

Input

hits:	(Input)	number of hits from embPatRestrictScan
isos:	(Input)	Allow isoschizomers
alpha:	(Input)	Sort alphabetically

Input & Output

(Modify)

list of hits from embPatRestrictScan

Returns

ajuint:

adjusted number of hits

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictStartCompare

Sort restriction site hits on the basis of start position

Synopsis

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

Input

a:	(Input)	First EmbPMatMatch hit
b:	(Input)	Second EmbPMatMatch hit

Returns

ajint:

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

Description

Sort restriction site hits on the basis of start position

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictCutCompare

Sort restriction site hits on the basis of cut position

Synopsis

Prototype

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

Input

a:	(Input)	First EmbPMatMatch hit
b:	(Input)	Second EmbPMatMatch hit

Returns

ajint:

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

Description

Sort restriction site hits on the basis of cut position

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictNameCompare

Sort restriction site hits on the basis of enzyme name

Synopsis

Prototype

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

Input

a:	(Input)	First EmbPMatMatch hit
b:	(Input)	Second EmbPMatMatch hit

Returns

ajint:

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

Description

Sort restriction site hits on the basis of enzyme name

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatRestrictMatch

Main Restriction function. Scans sequence and rejects unwanted cutters

Synopsis

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

Input

seq:	(Input)	sequence
begin:	(Input)	start position in sequence
end:	(Input)	end position in sequence
enzymes:	(Input)	comma separated list of REs or NULL for all
sitelen:	(Input)	minimum length of recognition site
plasmid:	(Input)	Circular DNA
ambiguity:	(Input)	Allow ambiguities
min:	(Input)	minimum number of true cuts
max:	(Input)	maximum number of true cuts
blunt:	(Input)	Allow blunt cutters
sticky:	(Input)	Allow sticky cutters
commercial:	(Input)	Allow Only report REs with a supplier
methyl:	(Input)	Mark methylated bases as 'N'

Input & Output

enzfile:	(Modify)	file pointer to .enz file
methfile:	(Modify)	file pointer to methylation data file
l:	(Modify)	list for (EmbPMatMatch) hits

Returns

ajuint:

number of hits

Description

Main Restriction function. Scans sequence and rejects unwanted cutters

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatGetType

Return the type of a pattern

Synopsis

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

Input

pattern:	(Input)	original pattern
mismatch:	(Input)	number of allowed mismatches
protein:	(Input)	true if protein

Output

cleanpat:	(Output)	cleaned pattern
m:	(Output)	real length of pattern
left:	(Output)	must match left begin
right:	(Output)	must match right

Returns

ajuint:

type of pattern

Description

Return the type of a pattern

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatCompile

Compile a pattern classified by embPatGetType

Synopsis

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

Input

type:	(Input)	pattern type
pattern:	(Input)	original pattern
mismatch:	(Input)	number of allowed mismatches

Output

plen:	(Output)	pattern length
buf:	(Output)	buffer for BMH and BYP search (can be -1)
off:	(Output)	offset buffer for B-Y/P search
sotable:	(Output)	buffer for SHIFT-OR
solimit:	(Output)	limit for SHIFT-OR
m:	(Output)	real length of pattern (from embPatGetType)
regexp:	(Output)	PCRE regexp string
skipm:	(Output)	skip buffer for Tarhio-Ukkonen

Returns

void:

No return value

Description

Compile a pattern classified by embPatGetType

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatFuzzSearch

Fuzzy search after embPatGetType and embPatCompile

Synopsis

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

Input

type:	(Input)	pattern type
begin:	(Input)	text displacement (1=start)
pattern:	(Input)	processed pattern
name:	(Input)	name associated with text
text:	(Input)	text
plen:	(Input)	pattern length
mismatch:	(Input)	number of allowed mismatches
left:	(Input)	must match left
right:	(Input)	must match right
sotable:	(Input)	buffer for SHIFT-OR
solimit:	(Input)	limit for SHIFT-OR
regexp:	(Input)	PCRE regexp string
skipm:	(Input)	skip buffer for Tarhio-Ukkonen-Bleasby
m:	(Input)	real pat length (from embPatGetType/embPatCompile)

Output

hits:	(Output)	number of hits
tidy:	(Output)	data to free

Input & Output

l:	(Modify)	list to push hits onto
buf:	(Modify)	buffer for BMH search
off:	(Modify)	offset buffer for B-Y/P search

Returns

void:

No return value

Description

Fuzzy search after embPatGetType and embPatCompile

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatCompileII

Compile a pattern classified by embPatGetType

Synopsis

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

Input

mismatch:

(Input)

number of allowed mismatches

Input & Output

thys:

(Modify)

Prosite pattern stucture

Returns

void:

No return value

Description

Compile a pattern classified by embPatGetType

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatFuzzSearchII

Fuzzy search after embPatGetType and embPatCompile

Synopsis

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

Input

begin:	(Input)	Sequence displacement (1=start)
name:	(Input)	Name associated with sequence
text:	(Input)	Sequence
mismatch:	(Input)	number of allowed mismatches

Output

hits:	(Output)	number of hits
tidy:	(Output)	data to free

Input & Output

thys:	(Modify)	Prosite pattern stucture
l:	(Modify)	List to push hits onto

Returns

void:

No return value

Description

Fuzzy search after embPatGetType and embPatCompile

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embPatGetTypeII

Return the type of a pattern

Synopsis

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

Input

pattern:	(Input)	Original pattern
mismatch:	(Input)	Number of allowed mismatches
protein:	(Input)	True if protein

Input & Output

thys:

(Modify)

Prosite pattern stucture

Returns

ajuint:

type of pattern

Description

Return the type of a pattern

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

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
AjPPatComp	thys	Modify	Prosite pattern stucture
ajuint	mismatch	Input	number of allowed mismatches
void		RETURN

embpat.c

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype