int main( int ac, char **av )
{
int *nlen;
static char **name, **seq;
double score;
extern double score_calc_for_score( int, char ** );
arguments( ac, av );
getnumlen( stdin );
rewind( stdin );
nlen = AllocateIntVec( njob );
name = AllocateCharMtx( njob, B+1 );
seq = AllocateCharMtx( njob, nlenmax+2 );
readData_pointer( stdin, name, nlen, seq );
if( !isaligned( njob, seq ) ) ErrorExit( "Not aligned." );
constants( njob, seq );
score = score_calc_for_score( njob, seq );
if( scoremtx == 0 ) score += offset;
fprintf( stdout, "score = %f\n", score );
if ( scoremtx == 0 ) fprintf( stdout, "JTT %dPAM\n", pamN );
else if( scoremtx == 1 ) fprintf( stdout, "Dayhoff( machigai ga aru )\n" );
else if( scoremtx == 2 ) fprintf( stdout, "M-Y\n" );
else if( scoremtx == -1 ) fprintf( stdout, "DNA 1:%d\n", kimuraR );
fprintf( stdout, "gap penalty = %+6.2f, %+6.2f, %+6.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
exit( 0 );
}
void CMPage::Clear(void)
{
if (!Is_Empty())
{
m_freeblock_num = m_allblock_num;
assert(isaligned(m_block, m_align_size) && "memory not aligned");
m_freeblock_head = (FreeBlock*)m_block;
m_freeblock_head->next = 0;
}
}
static errcode_t test_memalign(unsigned long align)
{
void *ptr = 0;
errcode_t retval;
retval = ext2fs_get_memalign(32, align, &ptr);
if (!retval && !isaligned(ptr, align))
retval = EINVAL;
free(ptr);
printf("tst_memalign(%lu) is %s\n", align,
retval ? error_message(retval) : "OK");
return retval;
}
void CMPage::Free(void* ptr)
{
// 检测Pool是否分配以及待释放指针是否为空, 以防止发生错误
if (!ptr) return;
if (Is_ContainsPointer(ptr) && isaligned(ptr, m_align_size))
{
// 将释放的内存还给Pool
freeblock((FreeBlock*)ptr);
}
else
{
assert(false && "object not allocated from this pool");
}
}
void CMPage::create(unsigned long block_size, unsigned long align_size)
{
unsigned long src_pagesize = Get_PageSize();
// 得到对齐后的一个block的内存大小，每个block必须大于sizeof(FreeBlock*)
m_block_size = Calc_AlignedSize(block_size, align_size);
m_align_size = align_size;
// 首先是维护FreeBlock指针占用的内存大小
//unsigned long pointersize = sizeof(FreeBlock*);
unsigned long maxfilledsize = m_align_size - 1;
if (m_block_size + maxfilledsize > DEFAULT_PAGESIZE)
{
m_page_size = m_block_size + maxfilledsize;
m_allblock_num = 1;
}
else
{
m_page_size = DEFAULT_PAGESIZE;
m_allblock_num = (m_page_size - maxfilledsize) / m_block_size;
}
m_freeblock_num = m_allblock_num;
// 如果原来的跟现在的内存一样大小 就不再分配
if (m_memory || src_pagesize != m_page_size)
{
if (m_memory)
{
::free(m_memory);
}
m_memory = ::malloc(m_page_size);
}
m_block = getaligned(m_memory, m_align_size);
// 检测分配内存是否满足内存对齐条件,
assert(isaligned(m_block, m_align_size) && "memory not aligned");
// 将FreeBlock链表头设置为分配的值
m_freeblock_head = (FreeBlock*)m_block;
m_freeblock_head->next = 0;
}
