Alpha Struct Reference

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Information about the alphabet used by seg. More...

Public Attributes
Int4	alphabet
	which alphabet, kProtAlphabet for proteins. More...
Int4	alphasize
	size of above alphabet. More...
double	lnalphasize
	nat. More...
Int4 *	alphaindex
	value in ncbistdaa. More...
unsigned char *	alphaflag
	array of bools to indicate that letter is (not) valid?? More...

Detailed Description

Information about the alphabet used by seg.

For proteins this version of seg uses ncbistdaa, This keeps track of those.

Definition at line 1324 of file blast_seg.c.

Member Data Documentation

alphabet

Int4 Alpha::alphabet

which alphabet, kProtAlphabet for proteins.

Definition at line 1326 of file blast_seg.c.

Referenced by s_AA20alphaStd().

alphaflag

unsigned char* Alpha::alphaflag

array of bools to indicate that letter is (not) valid??

Definition at line 1330 of file blast_seg.c.

Referenced by s_AA20alphaStd(), s_AlphaFree(), s_CompOn(), and s_ShiftWin1().

alphaindex

Int4* Alpha::alphaindex

value in ncbistdaa.

Definition at line 1329 of file blast_seg.c.

Referenced by s_AA20alphaStd(), s_AlphaFree(), s_CompOn(), and s_ShiftWin1().

alphasize

Int4 Alpha::alphasize

size of above alphabet.

Definition at line 1327 of file blast_seg.c.

Referenced by s_AA20alphaStd(), s_CompOn(), s_GetProb(), and s_StateOn().

lnalphasize

double Alpha::lnalphasize

nat.

log of size of above alphabet.

Definition at line 1328 of file blast_seg.c.

Referenced by s_AA20alphaStd(), and s_GetProb().

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The documentation for this struct was generated from the following file:

• src/algo/blast/core/blast_seg.c