embnmer.c

Function embNmerNuc2int

Encodes a word of a nucleic sequence into a unsigned ajlong ajint number. For a 4-byte unsigned ajlong ajint this will work if the word size is less than 16, otherwise there aren't enough bits to hold the number.

Synopsis

Prototype

ajulong embNmerNuc2int (
      const char* seq,
      ajint wordsize,
      ajint offset,
      AjBool* otherflag
);

Type Name Read/Write Description

const char* seq Input the sequence to use

ajint wordsize Input the size of word of sequence to convert to int

ajint offset Input the offset into the sequence of the start of the word

AjBool* otherflag Output set true if the sequence contains anything except A,G,C or T

ajulong RETURN the encoded word

Type	Name	Read/Write	Description
const char*	seq	Input	the sequence to use
ajint	wordsize	Input	the size of word of sequence to convert to int
ajint	offset	Input	the offset into the sequence of the start of the word
AjBool*	otherflag	Output	set true if the sequence contains anything except A,G,C or T
ajulong		RETURN	the encoded word

Input

seq:	(Input)	the sequence to use
wordsize:	(Input)	the size of word of sequence to convert to int
offset:	(Input)	the offset into the sequence of the start of the word

Output

otherflag:

(Output)

set true if the sequence contains anything except A,G,C or T

Returns

ajulong:

the encoded word

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embNmerInt2nuc

Decodes a unsigned long int number into a word of a nucleic sequence. The returned nucleic sequence is pre-pended to anything already in the string 'seq'.

Synopsis

Prototype

ajint embNmerInt2nuc (
      AjPStr* seq,
      ajint wordsize,
      ajulong value
);

Type Name Read/Write Description

AjPStr* seq Output the returned sequence

ajint wordsize Input the size of word to produce

ajulong value Input the number to decode

ajint RETURN not used

Type	Name	Read/Write	Description
AjPStr*	seq	Output	the returned sequence
ajint	wordsize	Input	the size of word to produce
ajulong	value	Input	the number to decode
ajint		RETURN	not used

Input

wordsize:	(Input)	the size of word to produce
value:	(Input)	the number to decode

Output

seq:

(Output)

the returned sequence

Returns

ajint:

not used

Description

Decodes a unsigned long int number into a word of a nucleic sequence. The returned nucleic sequence is pre-pended to anything already in the string 'seq'.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embNmerProt2int

Encodes a word of a protein sequence into a unsigned ajlong ajint number. For a 4-byte unsigned ajlong ajint this will work if the word size is less than 8, otherwise there aren't enough bits to hold the number.

Synopsis

Prototype

ajulong embNmerProt2int (
      const char* seq,
      ajint wordsize,
      ajint offset,
      AjBool* otherflag,
      AjBool ignorebz
);

Type	Name	Read/Write	Description
const char*	seq	Input	the sequence to use
ajint	wordsize	Input	the size of word of sequence to convert to int
ajint	offset	Input	the offset into the sequence of the start of the word
AjBool*	otherflag	Output	set true if the sequence contains anything other than valid amino acid codes
AjBool	ignorebz	Input	true if B and Z are to be treated as non-valid residues
ajulong		RETURN	the encoded word

Input

seq:	(Input)	the sequence to use
wordsize:	(Input)	the size of word of sequence to convert to int
offset:	(Input)	the offset into the sequence of the start of the word
ignorebz:	(Input)	true if B and Z are to be treated as non-valid residues

Output

otherflag:

(Output)

set true if the sequence contains anything other than valid amino acid codes

Returns

ajulong:

the encoded word

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embNmerInt2prot

Decodes a unsigned long int number into a word of a protein sequence. The returned protein sequence is pre-pended to anything already in the string 'seq'.

Synopsis

Prototype

ajint embNmerInt2prot (
      AjPStr* seq,
      ajint wordsize,
      ajulong value,
      AjBool ignorebz
);

Type Name Read/Write Description

AjPStr* seq Output the returned sequence

ajint wordsize Input the size of word to produce

ajulong value Input the number to decode

AjBool ignorebz Input true if B and Z are to be treated as non-valid residues

ajint RETURN not used

Type	Name	Read/Write	Description
AjPStr*	seq	Output	the returned sequence
ajint	wordsize	Input	the size of word to produce
ajulong	value	Input	the number to decode
AjBool	ignorebz	Input	true if B and Z are to be treated as non-valid residues
ajint		RETURN	not used

Input

wordsize:	(Input)	the size of word to produce
value:	(Input)	the number to decode
ignorebz:	(Input)	true if B and Z are to be treated as non-valid residues

Output

seq:

(Output)

the returned sequence

Returns

ajint:

not used

Description

Decodes a unsigned long int number into a word of a protein sequence. The returned protein sequence is pre-pended to anything already in the string 'seq'.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embNmerGetNoElements

Calculates the maximum number required to encode a sequence of size 'word'.

Synopsis

Prototype

AjBool embNmerGetNoElements (
      ajulong* no_elements,
      ajint word,
      AjBool seqisnuc,
      AjBool ignorebz
);

Type Name Read/Write Description

ajulong* no_elements Output the returned number

ajint word Input the size of word to produce

AjBool seqisnuc Input True is the sequence is nucleic, False if protein

AjBool ignorebz Input true if B and Z are to be treated as non-valid residues

AjBool RETURN True if the word is small enough to be encoded in an ajulong

Type	Name	Read/Write	Description
ajulong*	no_elements	Output	the returned number
ajint	word	Input	the size of word to produce
AjBool	seqisnuc	Input	True is the sequence is nucleic, False if protein
AjBool	ignorebz	Input	true if B and Z are to be treated as non-valid residues
AjBool		RETURN	True if the word is small enough to be encoded in an ajulong

Input

word:	(Input)	the size of word to produce
seqisnuc:	(Input)	True is the sequence is nucleic, False if protein
ignorebz:	(Input)	true if B and Z are to be treated as non-valid residues

Output

no_elements:

(Output)

the returned number

Returns

AjBool:

True if the word is small enough to be encoded in an ajulong

Description

Calculates the maximum number required to encode a sequence of size 'word'.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

embnmer.c

Function embNmerNuc2int

Synopsis

Prototype

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function embNmerInt2nuc

Synopsis

Prototype

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function embNmerProt2int

Synopsis

Prototype

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function embNmerInt2prot

Synopsis

Prototype

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Function embNmerGetNoElements

Synopsis

Prototype

Input

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability