chain.h File Reference

Provides object for storing named sequnces. More...

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Typedefs
typedef struct Chain	Chain
	Chain object used for storing named sequnces. More...

Functions
Chain *	chainCreate (char *name, int nameLen, char *string, int stringLen)
	Chain object constructor. More...
void	chainDelete (Chain *chain)
	Chain destructor. More...
char	chainGetChar (Chain *chain, int index)
	Chain char getter. More...
char	chainGetCode (Chain *chain, int index)
	Chain code getter. More...
int	chainGetLength (Chain *chain)
	Chain length getter. More...
const char *	chainGetName (Chain *chain)
	Chain name getter. More...
Chain *	chainCreateView (Chain *chain, int start, int end, int reverse)
	Creates a view to the chain object. More...
void	chainCopyCodes (Chain *chain, char *dest)
	Copies chain code to a buffer. More...
Chain *	chainDeserialize (char *bytes)
	Chain deserialization method. More...
void	chainSerialize (char **bytes, int *bytesLen, Chain *chain)
	Chain serialization method. More...

Detailed Description

Provides object for storing named sequnces.

Typedef Documentation

typedef struct Chain Chain

Chain object used for storing named sequnces.

Chain object is created from a named sequences and is used for alignment. Chain characters are coded with scorerEncode(char) function. Chain object provides view method for creating subchains and reverse subchains in constant time. On that behalf every chain object uses approximately 2 times more memory than the input sequence.

Function Documentation

void chainCopyCodes	(	Chain *	chain,
		char *	dest
	)

Copies chain code to a buffer.

Destination buffer should be allocated and its length should be greater or equal to chain length.

Parameters

chain	chain object
dest	pointer to the destination buffer

Chain* chainCreate	(	char *	name,
		int	nameLen,
		char *	string,
		int	stringLen
	)

Chain object constructor.

Method constructs the chain object with a given name and character sequence. All given data is copied. Any non-alphabetical characters in the sequence are ignored. All characters in the sequence are changed to uppercase.

Parameters

name	chain name
nameLen	chain name length
string	chain characters
stringLen	chain characters length

Returns

chain object

Chain* chainCreateView	(	Chain *	chain,
		int	start,
		int	end,
		int	reverse
	)

Creates a view to the chain object.

Method creates a subchain from the input chain. It doesn't copy the data since the original chain object is immutable. However the top parent chain object (one created via the constructor), should not be deleted before the views are deleted. Both the start and end indexes shoulde be greater than 1 and less than the chain length.

Parameters

chain	chain object
start	start index, inclusive
end	end index, inclusive
reverse	bool, 1 if the view should be reverse 0 otherwise

Returns

chain view

void chainDelete

(

Chain *

chain

)

Chain destructor.

Parameters

chain

chain object

Chain* chainDeserialize

(

char *

bytes

)

Chain deserialization method.

Method deserializes chain object from a byte buffer.

Parameters

bytes

byte buffer

Returns

chain object

char chainGetChar	(	Chain *	chain,
		int	index
	)

Chain char getter.

Method retrives the char from the index position. Index must be greater or equal to zero and less than chain length.

Parameters

chain	chain object
index	chain char index

Returns

chain char

char chainGetCode	(	Chain *	chain,
		int	index
	)

Chain code getter.

Method retrives the code from the index position. Index must be greater or equal to zero and less than chain length. Chain caracter is coded with the scorerEncode(char) function.

Parameters

chain	chain object
index	chain code index

Returns

chain code

int chainGetLength

(

Chain *

chain

)

Chain length getter.

Parameters

chain

chain object

Returns

length

const char* chainGetName

(

Chain *

chain

)

Chain name getter.

Parameters

chain

chain object

Returns

name

void chainSerialize	(	char **	bytes,
		int *	bytesLen,
		Chain *	chain
	)

Chain serialization method.

Method serializes chain object to a byte buffer.

Parameters

bytes	output byte buffer
bytesLen	output byte buffer length
chain	chain object