phmmMatrix Struct Reference

#include <pairHmm.h>

Collaboration diagram for phmmMatrix:

[legend]

Data Fields
char *	query
char *	target
int	querySize
int	targetSize
int	qDim
int	tDim
int	stateCount
int	stateSize
int	stateByteSize
phmmState *	states
phmmMommy *	allCells
int *	allScores

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Detailed Description

Definition at line 52 of file pairHmm.h.

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Field Documentation

char* phmmMatrix::query

Definition at line 55 of file pairHmm.h.

Referenced by affineAlign(), phmmMatrixNew(), phmmPrintTrace(), and xenAlignSmall().

char* phmmMatrix::target

Definition at line 56 of file pairHmm.h.

Referenced by affineAlign(), phmmMatrixNew(), phmmPrintTrace(), and xenAlignSmall().

int phmmMatrix::querySize

Definition at line 57 of file pairHmm.h.

Referenced by phmmMatrixNew(), and phmmPrintTrace().

int phmmMatrix::targetSize

Definition at line 58 of file pairHmm.h.

Referenced by phmmMatrixNew(), and phmmPrintTrace().

int phmmMatrix::qDim

Definition at line 59 of file pairHmm.h.

Referenced by affineAlign(), phmmFindMatrixIx(), phmmFindMommy(), phmmMatrixNew(), and xenAlignSmall().

int phmmMatrix::tDim

Definition at line 60 of file pairHmm.h.

Referenced by affineAlign(), phmmMatrixNew(), and xenAlignSmall().

int phmmMatrix::stateCount

Definition at line 61 of file pairHmm.h.

Referenced by affineAlign(), phmmMatrixNew(), and xenAlignSmall().

int phmmMatrix::stateSize

Definition at line 62 of file pairHmm.h.

Referenced by phmmFindMatrixIx(), and phmmMatrixNew().

int phmmMatrix::stateByteSize

Definition at line 63 of file pairHmm.h.

Referenced by phmmMatrixNew().

struct phmmState* phmmMatrix::states [read]

Definition at line 64 of file pairHmm.h.

Referenced by affineAlign(), phmmFindMommy(), phmmMatrixFree(), phmmMatrixNew(), phmmNameState(), and xenAlignSmall().

struct phmmMommy* phmmMatrix::allCells [read]

Definition at line 65 of file pairHmm.h.

Referenced by phmmFindMatrixIx(), phmmMatrixFree(), and phmmMatrixNew().

int* phmmMatrix::allScores

Definition at line 66 of file pairHmm.h.

Referenced by phmmMatrixFree(), and phmmMatrixNew().

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

• inc/pairHmm.h

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