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#ifndef _MOURISL_KMERCODE_HEADER
#define _MOURISL_KMERCODE_HEADER
#include <stdio.h>
#include "utils.h"
extern signed char nucToNum[26] ;
extern char numToNuc[26] ;
const int K_BLOCK_NUM = ( MAX_KMER_LENGTH - 1 ) / ( sizeof( uint64_t ) * 4 ) + 1 ;
#if MAX_KMER_LENGTH <= 32
class KmerCode
{
private:
int kmerLength ;
int invalidPos ; // The position contains characters other than A,C,G,T in the code
uint64_t code ;
uint64_t mask ;
public:
KmerCode()
{
}
KmerCode( int kl )
{
int i ;
kmerLength = kl ;
code = 0 ;
invalidPos = -1 ;
mask = 0 ;
for ( i = 0 ; i < kmerLength ; ++i )
{
mask = mask << 2 ;
mask = mask | 3 ;
}
}
KmerCode( const KmerCode& in )
{
kmerLength = in.kmerLength ;
invalidPos = in.invalidPos ;
mask = in.mask ;
code = in.code ;
}
void Restart() { code = 0ull ; invalidPos = -1 ; }
uint64_t GetCode() { return code ; }
int GetKmerLength() { return kmerLength ; }
bool IsValid()
{
/*if ( invalidPos != -1 )
{
printf( "hi\n") ;
}*/
return ( invalidPos == -1 ) ;
}
void Append( char c )
{
if ( invalidPos != -1 )
++invalidPos ;
code = ( ( code << 2ull ) & mask ) |
( (uint64_t)( nucToNum[ c - 'A' ] & 3 ) ) ;
if ( nucToNum[c - 'A'] == -1 )
{
invalidPos = 0 ;
}
if ( invalidPos >= kmerLength )
invalidPos = -1 ;
}
void Prepend( char c )
{
ShiftRight() ;
if ( nucToNum[c-'A'] == -1 )
{
invalidPos = kmerLength - 1 ;
}
code = ( code | ( (uint64_t)( nucToNum[c - 'A'] & 3 ) << ( 2ull * ( kmerLength - 1 ) ) ) ) & mask ;
}
inline void ShiftRight()
{
if ( invalidPos != -1 )
--invalidPos ;
code = ( code >> 2ull ) & ( mask >> 2ull ) ;
if ( invalidPos < 0 )
invalidPos = -1 ;
}
KmerCode& operator=( const KmerCode& in )
{
kmerLength = in.kmerLength ;
invalidPos = in.invalidPos ;
mask = in.mask ;
code = in.code ;
return *this ;
}
} ;
#else
class KmerCode
{
private:
int kmerLength ;
int invalidPos ; // The position contains characters other than A,C,G,T in the code
int largestBlock ;
uint64_t code[K_BLOCK_NUM] ;
uint64_t mask ;
public:
KmerCode()
{
}
KmerCode( int kl )
{
int i ;
kmerLength = kl ;
for ( i = 0 ; i < K_BLOCK_NUM ; ++i )
code[i] = 0 ;
invalidPos = -1 ;
mask = 0 ;
const int residual = ( kmerLength - 1 ) & ( sizeof( uint64_t ) * 4 - 1 ) ;
for ( i = 0 ; i <= residual ; ++i )
{
mask = mask << 2 ;
mask = mask | 3 ;
}
largestBlock = ( kmerLength - 1 ) / ( sizeof( uint64_t ) * 4 ) ;
}
KmerCode( const KmerCode& in )
{
kmerLength = in.kmerLength ;
invalidPos = in.invalidPos ;
largestBlock = in.largestBlock ;
mask = in.mask ;
for ( int i = 0 ; i < K_BLOCK_NUM ; ++i )
code[i] = in.code[i] ;
}
void Restart()
{
for ( int i = 0 ; i < K_BLOCK_NUM ; ++i )
code[i] = 0 ;
invalidPos = -1 ;
}
int GetCode( uint64_t outCode[] )
{
for ( int i = 0 ; i < K_BLOCK_NUM ; ++i )
outCode[i] = code[i] ;
return K_BLOCK_NUM ;
}
uint64_t GetCodeI( int index )
{
return code[index] ;
}
int GetKmerLength() { return kmerLength ; }
bool IsValid()
{
/*if ( invalidPos != -1 )
{
printf( "hi\n") ;
}*/
return ( invalidPos == -1 ) ;
}
// the bits are organsized:
// 4321 8765 ...
void Append( char c )
{
ShiftLeft() ;
code[0] |= ( (uint64_t)( nucToNum[ c - 'A' ] & 3 ) ) ;
if ( nucToNum[c - 'A'] == -1 )
{
invalidPos = 0 ;
}
}
void Prepend( char c )
{
ShiftRight() ;
if ( nucToNum[c-'A'] == -1 )
{
invalidPos = kmerLength - 1 ;
}
const uint64_t residual = ( kmerLength - 1 ) % ( sizeof( uint64_t ) * 4 ) ;
code[largestBlock] = ( code[largestBlock] | ( (uint64_t)( nucToNum[c - 'A'] & 3 ) << ( 2ull * ( residual ) ) ) ) & mask ;
}
void ShiftLeft()
{
if ( invalidPos != -1 )
++invalidPos ;
int i ;
for ( i = largestBlock ; i >= 0 ; --i )
{
code[i] = ( code[i] << (2ull) ) ;
if ( i > 0 )
{
uint64_t head = ( code[i - 1] >> (62ull ) ) & 3ull;
code[i] |= head ;
}
}
code[ largestBlock ] &= mask ;
if ( invalidPos >= kmerLength )
invalidPos = -1 ;
}
void ShiftRight()
{
if ( invalidPos != -1 )
--invalidPos ;
int i ;
for ( i = 0 ; i <= largestBlock ; ++i )
{
if ( i > 0 )
{
uint64_t tail = code[i] & 3ull ;
code[i - 1] |= ( tail << ( 2ull * 31 ) ) ;
}
code[i] = ( code[i] >> ( 2ull ) ) ;
}
code[ largestBlock ] &= ( mask >> 2ull ) ;
if ( invalidPos < 0 )
invalidPos = -1 ;
}
KmerCode& operator=( const KmerCode& in )
{
kmerLength = in.kmerLength ;
invalidPos = in.invalidPos ;
largestBlock = in.largestBlock ;
mask = in.mask ;
for ( int i = 0 ; i < K_BLOCK_NUM ; ++i )
code[i] = in.code[i] ;
return *this ;
}
} ;
#endif
#endif
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