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#include "CloneManager.h"
TCloneManager::TCloneManager ()
{
_success = false ;
}
TCloneManager::~TCloneManager ()
{
}
int TCloneManager::scan_item ( unsigned char *t , int a , TVector *v )
{
int b ;
wxString name , desc ;
a += 4 ;
// unsigned int strange1 = *((unsigned int*)(t+a)) ;
a += 4 ;
if ( t[a] == 8 )
{
while ( t[a] != 255 || t[a+1] != 255 ) a += 4 ;
return a ;
}
// unsigned int strange2 = *((unsigned int*)(t+a)) ;
a += 4 ;
unsigned int from = *((unsigned int*)(t+a)) ;
a += 4 ;
unsigned int to = *((unsigned int*)(t+a)) ;
a += 4 ;
for ( b = a ; t[b] >= 32 && b < a+8 ; b++ ) name += t[b] ;
a += 8 ;
for ( b = a ; t[b] ; b++ ) desc += t[b] ;
a = b ;
while ( a % 4 > 0 ) a++ ;
while ( t[a] != 255 && ( t[a] < 'A' || t[a] > 'Z' ) ) a += 4 ; // Ugly hack!
int dir = 1 ;
if ( to < from )
{
dir = -1 ;
int x = from ;
from = to ;
to = x ;
}
int type = VIT_MISC ;
if ( to - from > 80 ) type = VIT_GENE ;
else if ( name.Left(3).Lower() == _T("ori") ) type = VIT_REP_ORI ;
TVectorItem vi ( name , desc , from , to , type ) ;
vi.setDirection ( dir ) ;
v->items.push_back ( vi ) ;
return a ;
}
void TCloneManager::load ( wxString file )
{
wxFile f ( file , wxFile::read ) ;
long l = f.Length() ;
unsigned char *t = new unsigned char [l+5] ;
f.Read ( t , l ) ;
f.Close() ;
if ( t[0] != 26 || t[1] != 'S' || t[2] != 'E' || t[3] != 'S' )
{
delete t ;
return ;
}
int a ;
TVector *v = new TVector ;
wxString name = file.AfterLast('/').AfterLast('\\').BeforeLast('.') ;
wxString seq , desc ;
// Items
a = 12 ;
while ( t[a+2] == 0 && t[2+3] == 0 )
{
unsigned char a1 = t[a] ;
unsigned char a2 = t[a+1] ;
if ( a1 == 255 && a2 == 255 ) a = scan_item ( t , a , v ) ;
else
{
a += 8 ;
}
}
// Sequence
while ( t[a] >= 65 ) seq += t[a++] ;
// Rest
for ( a = l - 1 ; t[a-1] || t[a-2] ; a-- ) ;
for ( ; a < l ; a++ )
{
if ( t[a] == 10 ) continue ;
if ( t[a] == 13 || t[a] == 0 ) desc += '\n' ;
else desc += t[a] ;
}
// Set vector
v->setName ( name ) ;
v->setSequence ( seq ) ;
v->setDescription ( desc ) ;
if ( seq.length() > 3000 ) v->setCircular () ; // Guessing
_v.push_back ( v ) ;
_success = true ;
delete t ;
}
int TCloneManager::countVectors ()
{
return _v.size() ;
}
TVector *TCloneManager::getVector ( int a )
{
return _v[a] ;
}
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