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#include "SCFtype.h"
// Stuff copied from staden package
/*
* Basic type definitions
*/
typedef unsigned long int uint_4;
typedef signed long int int_4;
typedef unsigned short int uint_2;
typedef signed short int int_2;
typedef unsigned char uint_1;
typedef signed char int_1;
/** \typedef SCF_Header
\brief Type definition for the SCF_Header structure
*/
typedef struct {
uint_4 magic_number;
uint_4 samples; ///< Number of elements in Samples matrix
uint_4 samples_offset; ///< Byte offset from start of file
uint_4 bases; ///< Number of bases in Bases matrix
uint_4 bases_left_clip; ///< OBSOLETE: No. bases in left clip (vector)
uint_4 bases_right_clip; ///< OBSOLETE: No. bases in right clip (qual)
uint_4 bases_offset; ///< Byte offset from start of file
uint_4 comments_size; ///< Number of bytes in Comment section
uint_4 comments_offset; ///< Byte offset from start of file
char version[4]; ///< "version.revision", eg '3' '.' '0' '0'
uint_4 sample_size; ///< Size of samples in bytes 1=8bits, 2=16bits
uint_4 code_set; ///< code set used (but ignored!)
uint_4 private_size; ///< No. of bytes of Private data, 0 if none
uint_4 private_offset; ///< Byte offset from start of file
uint_4 spare[18]; ///< Unused
} SCF_Header;
/** \typedef SCF_Samples1
\brief Type definition for the SCF_Samples1 data
*/
typedef struct {
uint_1 sample_A; ///< Sample for A trace
uint_1 sample_C; ///< Sample for C trace
uint_1 sample_G; ///< Sample for G trace
uint_1 sample_T; ///< Sample for T trace
} SCF_Samples1;
/** \typedef SCF_Samples2
\brief Type definition for the SCF_Samples2 data
*/
typedef struct {
uint_2 sample_A; ///< Sample for A trace
uint_2 sample_C; ///< Sample for C trace
uint_2 sample_G; ///< Sample for G trace
uint_2 sample_T; ///< Sample for T trace
} SCF_Samples2 ;
/*
* Type definition for the sequence data
*/
typedef struct {
uint_4 peak_index; /* Index into Samples matrix for base posn */
uint_1 prob_A; /* Probability of it being an A */
uint_1 prob_C; /* Probability of it being an C */
uint_1 prob_G; /* Probability of it being an G */
uint_1 prob_T; /* Probability of it being an T */
char base; /* Called base character */
uint_1 spare[3]; /* Spare */
} SCF_Base;
// GENtle stuff
uint_4 get_real_uint4 ( uint_4 x )
{
unsigned char *c = (unsigned char*) (&x) ;
uint_4 u = 0 ;
u |= *(c+0) ;
u <<= 8 ;
u |= *(c+1) ;
u <<= 8 ;
u |= *(c+2) ;
u <<= 8 ;
u |= *(c+3) ;
return u ;
}
void make_real_uint4 ( uint_4 &x )
{
x = get_real_uint4 ( x ) ;
}
uint_2 get_real_uint2 ( uint_2 x )
{
unsigned char *c = (unsigned char*) (&x) ;
uint_2 ret = 0 ;
ret |= *(c+1) ;
ret <<= 8 ;
ret |= *(c+0) ;
return ret ;
}
SCFtype::SCFtype ()
{
}
bool SCFtype::parse ( wxString filename )
{
wxFile f ( filename , wxFile::read ) ;
long l = f.Length() ;
unsigned char *t = new unsigned char [l+15] ;
f.Read ( t , l ) ;
f.Close() ;
if ( *(t+0) != '.' || *(t+1) != 's' || *(t+2) != 'c' || *(t+3) != 'f' )
{
delete t ;
return false ; // No luck
}
SCF_Header *header = (SCF_Header*) t ;
wxString version ;
version += (*header).version[0] ;
version += (*header).version[1] ;
version += (*header).version[2] ;
version += (*header).version[3] ;
if ( (*header).version[0] < '3' )
{
wxMessageBox ( _T("Cannot read SFC prior to 3.0, this is ") + version ) ;
return false ;
}
// Requires SCF V3.0 from here on!
make_real_uint4 ( (*header).comments_size ) ;
make_real_uint4 ( (*header).comments_offset ) ;
make_real_uint4 ( (*header).bases ) ;
make_real_uint4 ( (*header).bases_offset ) ;
make_real_uint4 ( (*header).samples ) ;
make_real_uint4 ( (*header).samples_offset ) ;
make_real_uint4 ( (*header).sample_size ) ;
if ( (*header).samples == 0 || (*header).bases == 0 ) return false ; // Paranoia
unsigned char *c ;
unsigned int a ;
// Read comment
sd.comment.Empty() ;
for ( a = 0 , c = t + (*header).comments_offset ; a < (*header).comments_size ; a++ , c++ )
sd.comment += *c ;
// Preparing to read sequence information
void *v = t + (*header).bases_offset ;
unsigned long *ulp ;
sd.sequence.clear () ;
sd.seq.Empty () ;
for ( a = 0 , ulp = (unsigned long*) v ; a < (*header).bases ; a++ , ulp++ )
{
TSequencerDataSequenceItem si ;
si.peak_index = get_real_uint4 ( *ulp ) ;
sd.sequence.push_back ( si ) ;
}
// Reading sequence data
for ( a = 0 ; a < 5 ; a++ )
{
v = t + (*header).bases_offset + (*header).bases * ( 4 + a ) ;
read_data_block ( v , a ) ;
}
// Sorting sequence data; might be unnecessary
for ( a = 1 ; a < sd.sequence.size() ; a++ )
{
if ( sd.sequence[a-1].peak_index <= sd.sequence[a].peak_index ) continue ;
TSequencerDataSequenceItem d = sd.sequence[a-1] ;
sd.sequence[a-1] = sd.sequence[a] ;
sd.sequence[a] = d ;
a = 0 ;
}
/*
// Maximum trace data
unsigned long min = 9999 , max = 0 ;
for ( a = 0 ; a < sd.sequence.size() ; a++ )
{
if ( max < sd.sequence[a].peak_index ) max = sd.sequence[a].peak_index ;
if ( min > sd.sequence[a].peak_index ) min = sd.sequence[a].peak_index ;
}
if ( max >= sd.tracer.size() ) return false ; // Paranoia
*/
// Read tracer data
sd.tracer.clear () ;
while ( sd.tracer.size() < (*header).samples )
sd.tracer.push_back ( TSequencerDataTracerItem () ) ;
for ( a = 0 ; a < 4 ; a++ )
{
unsigned long offset = (*header).samples_offset + (*header).samples * a * (*header).sample_size ;
v = t + offset ;
read_tracer_block ( v , a , (*header).sample_size ) ;
}
// Fix tracer diff diff hell
for ( a = 0 ; a < 4 ; a++ )
fix_diff ( a ) ;
// Setup alternative tracer data set
for ( a = 0 ; a < 4 ; a++ ) sd.tracer2[a].clear () ;
for ( a = 0 ; a < sd.tracer.size() ; a++ )
{
TSequencerDataTracerItem ti = sd.tracer[a] ;
sd.tracer2[TRACER_ID_A].push_back ( ti.data[0] ) ;
sd.tracer2[TRACER_ID_C].push_back ( ti.data[1] ) ;
sd.tracer2[TRACER_ID_G].push_back ( ti.data[2] ) ;
sd.tracer2[TRACER_ID_T].push_back ( ti.data[3] ) ;
}
wxFile out ( _T("C:\\test.txt") , wxFile::write ) ;
for ( a = 0 ; a < sd.sequence.size() ; a++ )
{
out.Write ( wxString::Format ( _T("%5d: %5d %c\r\n") , a , sd.sequence[a].peak_index , sd.sequence[a].base ) ) ;
}
/*
// THE FOLLOWING MESS MIGHT PROVE USEFUL ONE DAY
// TO IMPORT SCF VERSIONS 1 AND 2 AS WELL
v += (*header).bases * 4
for ( a = 0 , base = (SCF_Base*) v ; a < (*header).bases ; a++ , base++ )
{
TSequencerDataSequenceItem si = sd[a] ;
// si.peak_index = get_real_uint4 ( (*base).peak_index ) ;
si.prob_a = (*base).prob_A ;
si.prob_c = (*base).prob_C ;
si.prob_g = (*base).prob_G ;
si.prob_t = (*base).prob_T ;
char c = 'A' ;
int prob = si.prob_a ;
if ( prob < si.prob_c ) { prob = si.prob_c ; c = 'C' ; }
if ( prob < si.prob_g ) { prob = si.prob_g ; c = 'G' ; }
if ( prob < si.prob_t ) { prob = si.prob_t ; c = 'T' ; }
sd.seq += c ;
si.base = (*base).base ;
sd[a] = si ;
// sd.sequence.push_back ( si ) ;
// out += wxString::Format ( _T("%d:%c\n\r\n") , si.peak_index , si.base ) ;
}
// Read samples
SCF_Samples1 *s1 = NULL ;
SCF_Samples2 *s2 = NULL ;
v = t + (*header).samples_offset ;
bool use_word = (*header).sample_size == 2 ;
if ( use_word ) s2 = (SCF_Samples2 *) v ;
else s1 = (SCF_Samples1 *) v ;
sd.tracer.clear () ;
for ( a = 0 ; a < 4 ; a++ ) sd.tracer2[a].clear () ;
for ( a = 0 ; a < (*header).samples ; a++ )
{
TSequencerDataTracerItem ti ;
ti.a = use_word ? get_real_uint2 ( s2->sample_A ) : s1->sample_A ;
ti.c = use_word ? get_real_uint2 ( s2->sample_C ) : s1->sample_C ;
ti.g = use_word ? get_real_uint2 ( s2->sample_G ) : s1->sample_G ;
ti.t = use_word ? get_real_uint2 ( s2->sample_T ) : s1->sample_T ;
// out += wxString::Format ( _T("%d,%d,%d,%d; ") , ti.a , ti.c , ti.g , ti.t ) ;
sd.tracer.push_back ( ti ) ;
sd.tracer2[TRACER_ID_A].push_back ( ti.a ) ;
sd.tracer2[TRACER_ID_C].push_back ( ti.c ) ;
sd.tracer2[TRACER_ID_G].push_back ( ti.g ) ;
sd.tracer2[TRACER_ID_T].push_back ( ti.t ) ;
if ( use_word ) s2++ ;
else s1++ ;
}
for ( a = 1 ; a < sd.sequence.size() ; a++ )
{
if ( sd.sequence[a-1].peak_index <= sd.sequence[a].peak_index ) continue ;
TSequencerDataSequenceItem d = sd.sequence[a-1] ;
sd.sequence[a-1] = sd.sequence[a] ;
sd.sequence[a] = d ;
a = 0 ;
}
*/
// wxMessageBox ( out ) ;
// wxMessageBox ( sd.comment ) ;
delete t ;
return true ;
}
void SCFtype::read_tracer_block ( void *v , unsigned int mode , unsigned int sample_size )
{
unsigned int a , samples = sd.tracer.size() ;
unsigned char *c = (unsigned char*) v ;
unsigned long lastx = 0 ;
for ( a = 0 ; a < samples ; a++ )
{
unsigned long x = 0 ;
if ( sample_size == 2 )
{
x |= (unsigned char) *(c+0) ;
x <<= 8 ;
x |= (unsigned char) *(c+1) ;
if ( x >= 32768 ) {
x = x - 65536 ;
}
c += 2 ;
}
else x = *c++ ;
sd.tracer[a].data[mode] = x ;
}
}
void SCFtype::read_data_block ( void *v , unsigned int mode )
{
unsigned int a , bases = sd.sequence.size() ;
unsigned char *c = (unsigned char*) v ;
for ( a = 0 ; a < bases ; a++ , c++ )
{
switch ( mode )
{
case 0 : sd.sequence[a].prob_a = *c ; break ;
case 1 : sd.sequence[a].prob_c = *c ; break ;
case 2 : sd.sequence[a].prob_g = *c ; break ;
case 3 : sd.sequence[a].prob_t = *c ; break ;
case 4 : sd.sequence[a].base = *c ; sd.seq += *c ; break ;
}
}
}
void SCFtype::fix_diff ( int mode )
{
signed long p_sample = 0;
unsigned long i , num_samples = sd.tracer.size() ;
for ( i = 0 ; i < num_samples ; i++ )
{
p_sample += sd.tracer[i].data[mode] ;
sd.tracer[i].data[mode] = p_sample ;
}
p_sample = 0 ;
for ( i = 0 ; i < num_samples ; i++ )
{
p_sample += sd.tracer[i].data[mode] ;
sd.tracer[i].data[mode] = p_sample ;
}
}
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