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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatSeqMatchFind

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

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatSeqMatchFindC

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

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatMatchGetLen

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

Synopsis

Prototype

ajint embPatMatchGetLen (
      const EmbPPatMatch data,
      ajint index
);

Input

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

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatMatchGetEnd

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

Synopsis

Prototype

ajint embPatMatchGetEnd (
      const EmbPPatMatch data,
      ajint index
);

Input

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

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatMatchGetNumber

Returns the number of pattern matches in the structure.

Synopsis

Prototype

ajint embPatMatchGetNumber (
      const EmbPPatMatch data
);

Input

data:(Input)results of match.

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatMatchGetStart

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

Synopsis

Prototype

ajint embPatMatchGetStart (
      const EmbPPatMatch data,
      ajint index
);

Input

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

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatMatchDel

Free all the memory from the pattern match search.

Synopsis

Prototype

void embPatMatchDel (
      EmbPPatMatch* pthis
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

Input

s:(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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictNew

Create a new restriction object

Synopsis

Prototype

EmbPPatRestrict embPatRestrictNew (
      void
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictDel

Delete a restriction object

Synopsis

Prototype

void embPatRestrictDel (
      EmbPPatRestrict* thys
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictReadEntry

Read next restriction enzyme from re file

Synopsis

Prototype

AjBool embPatRestrictReadEntry (
      EmbPPatRestrict re,
      AjPFile inf
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictScan

Scan a sequence with a restriction object

Synopsis

Prototype

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

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

l:(Modify)List to push hits to

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatKMPInit

Initialise a Knuth-Morris-Pratt pattern.

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatKMPSearch

Perform a Knuth-Morris-Pratt search

Synopsis

Prototype

ajint embPatKMPSearch (
      const AjPStr str,
      const AjPStr pat,
      ajint slen,
      ajint plen,
      const ajint* next,
      ajint 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
start:(Input)position within str to start search

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBMHInit

Initialise a Boyer-Moore-Horspool pattern.

Synopsis

Prototype

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

Input

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

Output

skip:(Output)offset table

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBMHSearch

Perform a Boyer-Moore-Horspool search

Synopsis

Prototype

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

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
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

l:(Modify)list to push to

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBYPInit

Initialise a Baeza-Yates,Perleberg pattern.

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatPushHit

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

Synopsis

Prototype

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

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

l:(Modify)list to push to

Returns

void:No return value

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBYPSearch

Perform a Baeza-Yates,Perleberg search.

Synopsis

Prototype

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

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

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

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.

Synopsis

Prototype

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

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

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.

Usage

ajcompl: ABC

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatSOInit

Initialise a Shift-Or pattern.

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatSOSearch

Perform a Shift-OR search.

Synopsis

Prototype

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

Input

str:(Input)search string
name:(Input)search string
first:(Input)first char of pattern
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

l:(Modify)list to push hits to

Returns

ajint:number of matches

Description

Perform a Shift-OR search.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBYGCInit

Initialise a Baeza-Yates Gonnet class pattern.

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBYGSearch

Perform a Baeza-Yates Gonnet search.

Synopsis

Prototype

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

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

l:(Modify)list to push hits to

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatTUInit

Initialise a Tarhio-Ukkonen search

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatTUSearch

Perform a Tarhio-Ukkonen search

Synopsis

Prototype

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

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

l:(Modify)list to push to

Returns

ajint:number of hits

Description

Perform a Tarhio-Ukkonen search

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatTUBInit

Initialise a Tarhio-Ukkonen-Bleasby search

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatTUBSearch

Perform a Tarhio-Ukkonen-Bleasby search

Synopsis

Prototype

ajint embPatTUBSearch (
      const AjPStr pat,
      const AjPStr text,
      ajint slen,
      ajint* const* skipm,
      ajint m,
      ajint k,
      ajint begin,
      AjPList l,
      AjBool amino,
      AjBool carboxyl,
      const AjPStr name,
      ajint 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

l:(Modify)list to push to

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatBruteForce

Match pattern to a sequence

Synopsis

Prototype

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

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

l:(Modify)list on which to push hits

Returns

ajint:number of hits

Description

Match pattern to a sequence

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatVariablePattern

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

Synopsis

Prototype

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

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

l:(Modify)list on which to push hits

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictPreferred

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

Synopsis

Prototype

void embPatRestrictPreferred (
      AjPList l,
      const AjPTable t
);

Input

t:(Input)table from embossre.equ file

Input & Output

l:(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

See Also

See other functions in this section

Availability

In release 3.0.0

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

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

Input

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

Input & Output

l:(Modify)list of hits from embPatRestrictScan

Returns

ajint: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.

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictStartCompare

Sort restriction site hits on the basis of start position

Synopsis

Prototype

ajint embPatRestrictStartCompare (
      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 start position

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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

See Also

See other functions in this section

Availability

In release 3.0.0

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatRestrictMatch

Main Restriction function. Scans sequence and rejects unwanted cutters

Synopsis

Prototype

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

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

Input & Output

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

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatGetType

Return the type of a pattern

Synopsis

Prototype

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

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

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatCompile

Compile a pattern classified by embPatGetType

Synopsis

Prototype

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

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 search
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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatFuzzSearch

Fuzzy search after embPatGetType and embPatCompile

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatCompileII

Compile a pattern classified by embPatGetType

Synopsis

Prototype

void embPatCompileII (
      AjPPatComp thys,
      ajint mismatch
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatFuzzSearchII

Fuzzy search after embPatGetType and embPatCompile

Synopsis

Prototype

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

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPatGetTypeII

Return the type of a pattern

Synopsis

Prototype

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

Input

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

Input & Output

thys:(Modify)Prosite pattern stucture

Returns

ajint: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

See Also

See other functions in this section

Availability

In release 3.0.0