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/*
* Copyright (c) Medical Research Council 2001. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*
*/
#ifndef _MUTLIB_H_
#define _MUTLIB_H_
#include <staden.h> /* For Read* structure */
#ifdef __cplusplus
extern "C" {
#endif
/*---------------------*/
/* Generic Definitions */
/*---------------------*/
/** Strand type */
typedef enum
{
MUTLIB_STRAND_FORWARD,
MUTLIB_STRAND_REVERSE
}mutlib_strand_t;
/** Input type */
typedef enum
{
MUTLIB_INPUT_REFERENCE,
MUTLIB_INPUT
}mutlib_input_t;
/** Trace type */
typedef struct
{
int New;
int ClipL;
int ClipR;
mutlib_strand_t Strand;
Read* Trace;
}mutlib_trace_t;
/** Sequence type */
typedef struct
{
int New;
int ClipL;
int ClipR;
mutlib_strand_t Strand;
char* Sequence;
}mutlib_sequence_t;
/** TC/TG experiment file tag */
typedef struct
{
char Type[5];
mutlib_strand_t Strand;
int Position[2];
char* Comment;
int Marked;
}mutlib_tag_t;
/** Algorithm result codes */
typedef enum
{
MUTLIB_RESULT_SUCCESS,
MUTLIB_RESULT_INVALID_INPUT,
MUTLIB_RESULT_INSUFFICIENT_OVERLAP,
MUTLIB_RESULT_INSUFFICIENT_DATA,
MUTLIB_RESULT_ALIGNMENT_FAILURE,
MUTLIB_RESULT_OUT_OF_MEMORY,
MUTLIB_RESULT_UNEXPECTED_EXCEPTION
}mutlib_result_t;
/*------------------------*/
/* TraceAlign Definitions */
/*------------------------*/
/** Trace align object */
typedef struct
{
/* Input objects owned by caller */
mutlib_trace_t Input;
mutlib_trace_t Reference[2];
/* Output objects owned by tracealign */
mutlib_trace_t Alignment[2];
mutlib_result_t ResultCode;
char* ResultString;
/* Internal objects owned by tracealign */
void* Cache;
int Initialised;
}tracealign_t;
/*----------------*/
/* TraceAlign API */
/*----------------*/
void TraceAlignInit( tracealign_t* ta );
void TraceAlignSetInput( tracealign_t* ta, mutlib_strand_t d, Read* r, int ql, int qr );
void TraceAlignSetReference( tracealign_t* ta, mutlib_strand_t d, Read* r, int ql, int qr );
mutlib_result_t TraceAlignExecute( tracealign_t* ta );
mutlib_result_t TraceAlignGetResultCode( tracealign_t* ta );
const char* TraceAlignGetResultString( tracealign_t* ta );
Read* TraceAlignGetAlignment( tracealign_t* ta, mutlib_input_t i, int* l, int* r );
void TraceAlignDestroy( tracealign_t* ta );
/*-----------------------*/
/* TraceDiff Definitions */
/*-----------------------*/
/** Maximum number of parameters */
#define TRACEDIFF_PARAMETERS 7
/* Trace difference parameters */
typedef enum
{
TRACEDIFF_PARAMETER_SENSITIVITY, /* Number of SD's from mean over noise window */
TRACEDIFF_PARAMETER_NOISE_THRESHOLD, /* Threshold below which is noise as % of max */
TRACEDIFF_PARAMETER_NOISE_WINDOW_LENGTH, /* Window in bases over which background noise level is computed */
TRACEDIFF_PARAMETER_PEAK_ALIGNMENT, /* Upper/lower peak centre alignment threshold in bases */
TRACEDIFF_PARAMETER_PEAK_WIDTH_MAXIMUM, /* Threshold in bases above which peak is considered to be too wide */
TRACEDIFF_PARAMETER_COMPLEMENT_TAGS, /* Complement reverse strand tags? */
TRACEDIFF_PARAMETER_YSCALE /* Scale traces in Y before differencing? */
}tracediff_parameter_t;
/** Trace difference algorithms */
typedef enum
{
/* New algorithms should be powers of 2 */
TRACEDIFF_ALGORITHM_DEFAULT = 1,
TRACEDIFF_ALGORITHM_DEFAULT_DIFFERENCE_ONLY = 2
}tracediff_algorithm_t;
/** Trace difference object */
typedef struct
{
/* Input objects owned by caller */
tracealign_t Alignment;
double Parameter[TRACEDIFF_PARAMETERS];
/* Output objects owned by tracediff */
mutlib_tag_t* Tag;
int TagCount;
Read* Difference;
int DifferenceLeft;
int DifferenceRight;
mutlib_result_t ResultCode;
char* ResultString;
/* Internal objects owned by tracediff */
int Initialised;
}tracediff_t;
/*---------------*/
/* TraceDiff API */
/*---------------*/
void TraceDiffInit( tracediff_t* td );
void TraceDiffSetParameter( tracediff_t* td, tracediff_parameter_t p, double v );
double TraceDiffGetParameter( tracediff_t* td, tracediff_parameter_t p );
void TraceDiffSetReference( tracediff_t* td, Read* w, mutlib_strand_t d, int ql, int qr );
void TraceDiffSetInput( tracediff_t* td, Read* i, mutlib_strand_t d, int ql, int qr );
mutlib_result_t TraceDiffExecute( tracediff_t* td, tracediff_algorithm_t a );
void TraceDiffDestroy( tracediff_t* td );
mutlib_result_t TraceDiffGetResultCode( tracediff_t* td );
const char* TraceDiffGetResultString( tracediff_t* td );
Read* TraceDiffGetDifference( tracediff_t* td, int* dl, int* dr );
int TraceDiffGetTagCount( tracediff_t* td );
mutlib_tag_t* TraceDiffGetTag( tracediff_t* td, int n );
/*---------------------*/
/* MutScan Definitions */
/*---------------------*/
/** Maximum number of parameters */
#define MUTSCAN_PARAMETERS 7
/** Mutation scanning parameters */
typedef enum
{
MUTSCAN_PARAMETER_ALIGNFAIL_THRESHOLD, /* Reports alignment failure after n mutations */
MUTSCAN_PARAMETER_COMPLEMENT_TAGS, /* Complement reverse strand tags? */
MUTSCAN_PARAMETER_HETSNR_THRESHOLD, /* SNR below which mutations are considered to be heterozygotes */
MUTSCAN_PARAMETER_PEAKDROP_LOWER, /* Lower peak height drop threshold in percent */
MUTSCAN_PARAMETER_NOISE_THRESHOLD, /* Noise floor threshold as percent of maximum peak height */
MUTSCAN_PARAMETER_PEAKDROP_UPPER, /* Upper peak height drop threshold in percent */
MUTSCAN_PARAMETER_SEARCH_WINDOW /* Search window to find corresponding peaks in bases */
}mutscan_parameter_t;
/** Mutscan object */
typedef struct
{
/* Input objects owned by caller */
mutlib_trace_t InputTrace;
mutlib_trace_t ReferenceTrace[2];
double Parameter[MUTSCAN_PARAMETERS];
/* Output objects owned by mutscan */
mutlib_tag_t* Tag;
int TagCount;
mutlib_result_t ResultCode;
char* ResultString;
/* Internal objects owned by mutscan */
int Initialised;
}mutscan_t;
/*-------------*/
/* MutScan API */
/*-------------*/
void MutScanInit( mutscan_t* ms );
void MutScanSetParameter( mutscan_t* ms, mutscan_parameter_t p, double v );
double MutScanGetParameter( mutscan_t* ms, mutscan_parameter_t p );
void MutScanSetReference( mutscan_t* ms, mutlib_strand_t d, Read* r, int ql, int qr );
void MutScanSetInput( mutscan_t* ms, mutlib_strand_t d, Read* i, int ql, int qr );
mutlib_result_t MutScanExecute( mutscan_t* ms );
void MutScanDestroy( mutscan_t* ms );
mutlib_result_t MutScanGetResultCode( mutscan_t* ms );
const char* MutScanGetResultString( mutscan_t* ms );
int MutScanGetTagCount( mutscan_t* ms );
mutlib_tag_t* MutScanGetTag( mutscan_t* ms, int n );
#ifdef __cplusplus
}
#endif
#endif
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