void init_move_tables(void) {
unsigned row;
memset(row_left_table, 0, sizeof(row_left_table));
memset(row_right_table, 0, sizeof(row_right_table));
memset(col_up_table, 0, sizeof(col_up_table));
memset(col_down_table, 0, sizeof(col_down_table));
for(row = 0; row < 65536; row++) {
unsigned int line[4] = {row & 0xf, (row >> 4) & 0xf, (row >> 8) & 0xf, (row >> 12) & 0xf};
row_t result;
int i, j;
/* execute a move to the left */
for(i=0; i<3; i++) {
for(j=i+1; j<4; j++) {
if(line[j] != 0)
break;
}
if(j == 4)
break; // no more tiles to the right
if(line[i] == 0) {
line[i] = line[j];
line[j] = 0;
i--; // retry this entry
} else if(line[i] == line[j] && line[i] != 0xf) {
line[i]++;
line[j] = 0;
}
}
result = (line[0]) | (line[1] << 4) | (line[2] << 8) | (line[3] << 12);
row_left_table[row] = row ^ result;
row_right_table[reverse_row(row)] = reverse_row(row) ^ reverse_row(result);
col_up_table[row] = unpack_col(row) ^ unpack_col(result);
col_down_table[reverse_row(row)] = unpack_col(reverse_row(row)) ^ unpack_col(reverse_row(result));
}
}
/* Core algorithm */
int cluster (FILE *fw, Edge **el, int n)
{
int block_id = 0;
Block **bb;
int allocated = po->SCH_BLOCK;
AllocArray(bb, allocated);
Edge *e;
Block *b;
struct dyStack *genes, *scores, *b_genes, *allincluster;
int i, j, k, components;
AllocArray(profile, cols);
for (j = 0; j < cols; j++) AllocArray(profile[j], sigma);
genes = dsNew(rows);
scores = dsNew(rows);
allincluster = dsNew(rows);
bool *candidates;
AllocArray(candidates, rows);
e = *el; i = 0;
while (i++ < n)
{
e = *el++;
/*printf("a:%d b:%d score:%d\n",e->gene_one,e->gene_two,e->score);*/
/* check if both genes already enumerated in previous blocks */
bool flag = TRUE;
/* speed up the program if the rows bigger than 200 */
if (rows > 200)
{
if ( isInStack(allincluster,e->gene_one) && isInStack(allincluster,e->gene_two) )
flag = FALSE;
}
else
{
flag = check_seed(e, bb, block_id);
}
if (!flag) continue;
for (j = 0; j < cols; j++)
for (k = 0; k < sigma; k++) profile[j][k] = 0;
AllocVar(b);
b->score = MIN(2, e->score);
/* initialize the stacks genes and scores */
int ii;
dsClear(genes);
dsClear(scores);
for(ii = 0; ii < rows; ii ++)
{
dsPush(genes,-1);
dsPush(scores,-1);
}
dsClear(genes);
dsClear(scores);
dsPush(genes, e->gene_one);
dsPush(genes, e->gene_two);
dsPush(scores, 1);
dsPush(scores, b->score);
/* branch-and-cut condition for seed expansion */
int cand_threshold = floor(po->COL_WIDTH * po->TOLERANCE);
if (cand_threshold < 2) cand_threshold = 2;
/* maintain a candidate list to avoid looping through all rows */
for (j = 0; j < rows; j++) candidates[j] = TRUE;
candidates[e->gene_one] = candidates[e->gene_two] = FALSE;
components = 2;
/* expansion step, generate a bicluster without noise */
block_init(e, b, genes, scores, candidates, cand_threshold, &components, allincluster);
/* track back to find the best score that which genes makes it */
for(k = 0; k < components; k++)
if ((dsItem(scores,k) == b->score)&&(dsItem(scores,k+1)!= b->score)) break;
components = k + 1;
int ki;
for (ki=0; ki < rows; ki++)
candidates[ki] = TRUE;
for (ki=0; ki < components - 1 ; ki++)
{
seed_update(arr_c[dsItem(genes,ki)]);
candidates[dsItem(genes,ki)] = FALSE;
}
candidates[dsItem(genes,k)] = FALSE;
genes->top = k ;
int cnt = 0;
bool *colcand;
AllocArray(colcand, cols);
for(ki = 0; ki < cols; ki++) colcand[ki] = FALSE;
/* add columns satisfy the conservative r */
seed_current_modify(arr_c[dsItem(genes,k)], colcand, &cnt, components);
/* add some new possible genes */
int m_cnt;
for ( ki = 0; ki < rows; ki++)
{
m_cnt = intersect_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt* po->TOLERANCE)) )
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
b->block_rows_pre = components;
/* add genes that negative regulated to the consensus */
for ( ki = 0; ki < rows; ki++)
{
m_cnt = reverse_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt * po->TOLERANCE)) )
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
free(colcand);
/* save the current cluster*/
b_genes = dsNew(b->block_rows_pre);
for (ki = 0; ki < b->block_rows_pre; ki++)
dsPush(b_genes, dsItem(genes,ki));
/* store gene arrays inside block */
b->genes = dsNew(components);
b->conds = dsNew(cols);
scan_block(b_genes, b);
if (b->block_cols == 0) continue;
b->block_rows = components;
b->score = b->block_rows * b->block_cols;
dsClear(b->genes);
for ( ki=0; ki < components; ki++)
dsPush(b->genes,dsItem(genes,ki));
for(ki = 0; ki < components; ki++)
if(!isInStack(allincluster, dsItem(genes,ki))) dsPush(allincluster,dsItem(genes,ki));
bb[block_id++] = b;
/* reaching the results number limit */
if (block_id == po->SCH_BLOCK) break;
verboseDot();
}
putchar('\n');
/* free-up the candidate list */
free(candidates);
free(allincluster);
return report_blocks(fw, bb, block_id);
}
/* Core algorithm */
int cluster (FILE *fw, Edge **el, int n)
{
int block_id = 0;
Block **bb;
int allocated = po->SCH_BLOCK;
AllocArray(bb, allocated);
Edge *e;
Block *b;
struct dyStack *genes, *scores, *b_genes, *allincluster;
int i, j, k, components;
AllocArray(profile, cols);
for (j = 0; j < cols; j++)
AllocArray(profile[j], sigma);
genes = dsNew(rows);
scores = dsNew(rows);
allincluster = dsNew(rows);
bool *candidates;
AllocArray(candidates, rows);
e = *el;
i = 0;
while (i++ < n)
{
/*printf ("%d\n",i);*/
e = *el++;
/* check if both genes already enumerated in previous blocks */
bool flag = TRUE;
/* speed up the program if the rows bigger than 200 */
if (rows > 250)
{
if ( isInStack(allincluster,e->gene_one) && isInStack(allincluster,e->gene_two) )
flag = FALSE;
else if ((po->IS_TFname)&&(e->gene_one!= TFindex)&&(e->gene_two!=TFindex))
flag = FALSE;
else if ((po->IS_list)&&(!sublist[e->gene_one] || !sublist[e->gene_two]))
flag =FALSE;
}
else
{
flag = check_seed(e, bb, block_id);
if ((po->IS_TFname)&&(e->gene_one!= TFindex)&&(e->gene_two!=TFindex))
flag = FALSE;
if ((po->IS_list)&&(!sublist[e->gene_one] || !sublist[e->gene_two]))
flag = FALSE;
}
if (!flag) continue;
for (j = 0; j < cols; j++)
for (k = 0; k < sigma; k++)
profile[j][k] = 0;
/*you must allocate a struct if you want to use the pointers related to it*/
AllocVar(b);
/*initial the b->score*/
b->score = MIN(2, e->score);
/* initialize the stacks genes and scores */
int ii;
dsClear(genes);
dsClear(scores);
for(ii = 0; ii < rows; ii ++)
{
dsPush(genes,-1);
dsPush(scores,-1);
}
dsClear(genes);
dsClear(scores);
/*printf ("%d\t%d\n",e->gene_one,e->gene_two);*/
dsPush(genes, e->gene_one);
dsPush(genes, e->gene_two);
dsPush(scores, 1);
dsPush(scores, b->score);
/* branch-and-cut condition for seed expansion */
int cand_threshold = floor(po->COL_WIDTH * po->TOLERANCE);
if (cand_threshold < 2)
cand_threshold = 2;
/* maintain a candidate list to avoid looping through all rows */
for (j = 0; j < rows; j++)
candidates[j] = TRUE;
candidates[e->gene_one] = candidates[e->gene_two] = FALSE;
components = 2;
/* expansion step, generate a bicluster without noise */
block_init(e, b, genes, scores, candidates, cand_threshold, &components, allincluster);
/* track back to find the genes by which we get the best score*/
for(k = 0; k < components; k++)
{
/* printf ("******%d\t%d\n",dsItem(scores,k),b->score);*/
if ((dsItem(scores,k) == b->score)&&(dsItem(scores,k+1)!= b->score)) break;
}
components = k + 1;
/*printf ("%d",components);*/
int ki;
for (ki=0; ki < rows; ki++)
candidates[ki] = TRUE;
for (ki=0; ki < components - 1 ; ki++)
{
seed_update(arr_c[dsItem(genes,ki)]);
candidates[dsItem(genes,ki)] = FALSE;
}
candidates[dsItem(genes,k)] = FALSE;
genes->top = k ;
int cnt = 0;
bool *colcand;
AllocArray(colcand, cols);
for(ki = 0; ki < cols; ki++)
colcand[ki] = FALSE;
/* add columns satisfy the conservative r */
seed_current_modify(arr_c[dsItem(genes,k)], colcand, &cnt, components);
/* add some new possible genes */
int m_cnt=0;
continuous KL_score=0;
discrete *sub_array;
for ( ki = 0; ki < rows; ki++)
{
if (po->IS_list && !sublist[ki]) continue;
m_cnt = intersect_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt* po->TOLERANCE)) )
{
sub_array = get_intersect_row(colcand,arr_c[dsItem(genes,0)],arr_c[ki],m_cnt);
KL_score = get_KL (sub_array, arr_c[ki], m_cnt, cols);
/*printf ("%d\t%.2f\n",m_cnt,KL_score);*/
if (KL_score>=b->significance * po->TOLERANCE)
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
}
b->block_rows_pre = components;
/* add genes that negative regulated to the consensus */
for ( ki = 0; ki < rows; ki++)
{
if (po->IS_list && !sublist[ki]) continue;
m_cnt = reverse_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt * po->TOLERANCE)) )
{
sub_array = get_intersect_reverse_row(colcand,arr_c[dsItem(genes,0)],arr_c[ki],m_cnt);
KL_score = get_KL (sub_array, arr_c[ki], m_cnt, cols);
if (KL_score>=b->significance * po->TOLERANCE)
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
}
free(colcand);
/* save the current cluster*/
b_genes = dsNew(b->block_rows_pre);
for (ki = 0; ki < b->block_rows_pre; ki++)
dsPush(b_genes, dsItem(genes,ki));
/* store gene arrays inside block */
b->genes = dsNew(components);
b->conds = dsNew(cols);
scan_block(b_genes, b);
if (b->block_cols == 0) continue;
b->block_rows = components;
b->score = b->score;
/* b->score = b->block_rows * b->block_cols; */
dsClear(b->genes);
for ( ki=0; ki < components; ki++)
dsPush(b->genes,dsItem(genes,ki));
for(ki = 0; ki < components; ki++)
if(!isInStack(allincluster, dsItem(genes,ki)))
dsPush(allincluster,dsItem(genes,ki));
/*save the current block b to the block list bb so that we can sort the blocks by their score*/
bb[block_id++] = b;
/* reaching the results number limit */
if (block_id == po->SCH_BLOCK) break;
verboseDot();
}
/* writes character to the current position in the standard output (stdout) and advances the internal file position indicator to the next position.
* It is equivalent to putc(character,stdout).*/
putchar('\n');
/* free-up the candidate list */
free(candidates);
free(allincluster);
block_enrichment(fw, bb, block_id);
return report_blocks(fw, bb, block_id);
}
}
/* Read the .block file, get components and colcand */
void read_and_solve_blocks(FILE *fb, const char *fn)
{
init_expand();
size_t n;
int col;
char *line = NULL;
int bnumber = 0;
struct dyStack *ge, *co;
int i, components, m_cnt;
bool *colcand;
bool *candidates;
Block *b;
AllocVar(b);
AllocArray(colcand, another_cols);
AllocArray(candidates, another_rows);
ge = dsNew(another_rows);
co = dsNew(another_cols);
FILE *fo = mustOpen(fn, "w");
/* main course starts here */
while (getline(&line, &n, fb) != -1)
{
/* fast forward to a line that contains BC*/
/* strncmp compares up to num characters of the C string str1 to those of the C string str2
* strncmp ( const char * str1, const char * str2, size_t num )*/
while (strncmp(line, "BC", 2)!=0)
{
if (getline(&line, &n, fb)==-1)
exit(0);
}
components = 0;
col = 0;
dsClear(ge);
dsClear(co);
for (i=0; i< another_cols; i++)
colcand[i] = FALSE;
for (i=0; i< another_rows; i++)
candidates[i] = TRUE;
/* read genes from block */
getline(&line, &n, fb);
atom = strtok(line, delims);
atom = strtok(NULL, delims);
while((atom = strtok(NULL, delims)) != NULL)
{
/* look up for genes number */
if (strlen(atom) == 0) continue;
for(i=0; i<another_rows; i++)
{
if (strcmp(atom ,another_genes[i]) == 0) break;
}
candidates[i] = FALSE;
dsPush(ge, i);
components++;
}
/* read conditions from block */
getline(&line, &n, fb);
atom = strtok(line, delims);
atom = strtok(NULL, delims);
while((atom = strtok(NULL, delims)) != NULL)
{
/*if (strlen(atom) < 5) break;*/
if (strlen(atom) == 0) continue;
for(i=0; i<another_cols; i++)
if (strcmp(atom, another_conds[i]) == 0) break;
colcand[i] = TRUE;
dsPush(co, i);
col++;
}
b->block_rows_pre = components;
/* add some possible genes */
for( i = 0; i < another_rows; i++)
{
m_cnt = intersect_row(colcand, another_arr_c[dsItem(ge,0)], another_arr_c[i], another_cols);
printf ("%d\n",m_cnt);
if( candidates[i] && (m_cnt >= (int)floor( (double)col * po->TOLERANCE)) )
{
dsPush(ge,i);
components++;
candidates[i] = FALSE;
}
}
/* add genes that negative regulated to the consensus */
for( i = 0; i < another_rows; i++)
{
m_cnt = reverse_row(colcand, another_arr_c[dsItem(ge,0)], another_arr_c[i], another_cols);
if( candidates[i] && (m_cnt >= (int)floor( (double)col * po->TOLERANCE)) )
{
dsPush(ge,i);
components++;
candidates[i] = FALSE;
}
}
if(dsSize(ge) > 1)
{
store_block(b, ge, co);
/*another_print_bc(fo, b, bnumber);*/
print_bc(fo, b, bnumber++);
}
