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.

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

From EMBOSS 1.0.0

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'.

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

From EMBOSS 1.0.0

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.

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

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

From EMBOSS 1.0.0

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'.

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

From EMBOSS 1.0.0

Function embNmerGetNoElements

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

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

From EMBOSS 1.0.0