ajpat

Data type AjPPatBYPNode

Attributes

Name	Type	Description
next	struct AjSPatBYPNode*	Pointer to next node
offset	ajint	Offset
Padding	char[4]	Padding to alignment boundary

Data type AjPPatComp

Alias name(s)

Name
AjSPatComp
AjOPatComp

Attributes

Name	Type	Description
pattern	AjPStr	Prosite pattern string
type	ajuint	Prosite pattern compile type
plen	ajuint	Prosite pattern length
buf	ajint*	Buffer for BMH search (can be -1)
off	AjOPatBYPNode[AJALPHA]	Offset buffer for B-Y/P search
sotable	ajuint*	Buffer for SHIFT-OR
solimit	ajuint	Limit for BMH search
m	ajuint	Real length of pattern (from embPatGetType)
regex	AjPStr	PCRE regexp string
skipm	ajuint**	Skip buffer for Tarhio-Ukkonen
amino	AjBool	Must match left begin
carboxyl	AjBool	Must match right

Data type AjPPatternSeq

Holds definition of feature pattern. Regular expression patterns ignore mismatch value.

Alias name(s)

Name
AjSPatternSeq
AjOPatternSeq

Attributes

Name	Type	Description
Name	AjPStr	Name.
Pattern	AjPStr	Pattern in string format.
Compiled	void*	Compiled version of the pattern.
Protein	AjBool	True if protein pattern
Mismatch	ajuint	Mismatch value.

Constructor(s)

Name	Description
ajPatternSeqNew	Default constructor

Destructor(s)

Name	Description
ajPatternSeqDel	Default destructor

Operator(s)

Name	Description
ajPatternSeqGetName	Returns name.
ajPatternSeqGetPattern	Returns pattern in string format.
ajPatternSeqGetCompiled	Returns pointer to compiled pattern.
ajPatternSeqGetType	Returns type as integer value.
ajPatternSeqGetMismatch	Return mismatch value.

Data type AjPPatternRegex

Holds definition of feature pattern. Regular expression patterns ignore mismatch value.

Alias name(s)

Name
AjSPatternRegex
AjOPatternRegex

Attributes

Name	Type	Description
Name	AjPStr	Name.
Pattern	AjPStr	Pattern in string format.
Compiled	AjPRegexp	Compiled version of the pattern.
Type	ajuint	Type.
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajPatternRegexNew	Default constructor

Destructor(s)

Name	Description
ajPatternRegexDel	Default destructor

Operator(s)

Name	Description
ajPatternRegexGetName	Returns name.
ajPatternRegexGetPattern	Returns pattern in string format.
ajPatternRegexGetCompiled	Returns pointer to compiled pattern.
ajPatternRegexGetType	Returns type as integer value.

Data type AjPPatlistSeq

Holds list of feature patterns and general information of them.

Alias name(s)

Name
AjSPatlistSeq
AjOPatlistSeq

Attributes

Name	Type	Description
Patlist	AjPList	List for patterns.
Iter	AjIList	List iterator.
Protein	AjBool	True if protein
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajPatlistNew	Default constructor.

Destructor(s)

Name	Description
ajPatlistDel	Default destructor.

Modifier(s)

Name	Description
ajPatlistRegexRead	Reads the pattern file and fills the list.
ajPatlistSeqRead	Reads the pattern file and fills the list.
ajPatlistRewind	Restarts the iteration loop.
ajPatlistAdd	Adds new pattern into list.

Operator(s)

Name	Description
ajPatlistGetNext	Gets the next pattern from file and returns true if available and false if not.

Data type AjPPatlistRegex

Holds list of feature patterns and general information of them.

Alias name(s)

Name
AjSPatlistRegex
AjOPatlistRegex

Attributes

Name	Type	Description
Patlist	AjPList	List for patterns.
Iter	AjIList	List iterator.
Type	ajuint	Type of expression
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajPatlistNew	Default constructor.

Destructor(s)

Name	Description
ajPatlistDel	Default destructor.

Modifier(s)

Name	Description
ajPatlistRegexRead	Reads the pattern file and fills the list.
ajPatlistSeqRead	Reads the pattern file and fills the list.
ajPatlistRewind	Restarts the iteration loop.
ajPatlistAdd	Adds new pattern into list.

Operator(s)

Name	Description
ajPatlistGetNext	Gets the next pattern from file and returns true if available and false if not.