void overlapping_grid_input<COARSEG,FINEG,OVLP>::init(COARSEG const& cg,
std::string const& basenm_)
{
the_coarse_grid = &cg;
basenm = basenm_;
the_fine_grid.init(basenm + ".grid");
init_overlap();
}
static void bdinit (struct spotstr *bp)
{
_movenum = 1;
// mark the borders as such
struct spotstr* sp = bp;
for (int i = BSZ2; --i >= 0; ++sp) {
sp->s_occ = BORDER; // top border
sp->s_flg = BFLAGALL;
}
// fill entire board with EMPTY spots
memset(_frames, 0, sizeof(_frames));
struct combostr* cbp = _frames;
for (unsigned j = 0; ++j < BSZ1; ++sp) { // for each row
for (unsigned i = 0; ++i < BSZ1; ++sp) { // for each column
sp->s_occ = EMPTY;
sp->s_flg = 0;
sp->s_wval = 0;
if (j < 5) { // directions 1, 2, 3 are blocked
sp->s_flg |= (BFLAG << 1) | (BFLAG << 2) | (BFLAG << 3);
sp->s_fval[BLACK][1].s = MAXCOMBO;
sp->s_fval[BLACK][2].s = MAXCOMBO;
sp->s_fval[BLACK][3].s = MAXCOMBO;
sp->s_fval[WHITE][1].s = MAXCOMBO;
sp->s_fval[WHITE][2].s = MAXCOMBO;
sp->s_fval[WHITE][3].s = MAXCOMBO;
} else if (j == 5) { // five spaces, blocked on one side
sp->s_fval[BLACK][1].s = 0x500;
sp->s_fval[BLACK][2].s = 0x500;
sp->s_fval[BLACK][3].s = 0x500;
sp->s_fval[WHITE][1].s = 0x500;
sp->s_fval[WHITE][2].s = 0x500;
sp->s_fval[WHITE][3].s = 0x500;
} else { // six spaces, not blocked
sp->s_fval[BLACK][1].s = 0x401;
sp->s_fval[BLACK][2].s = 0x401;
sp->s_fval[BLACK][3].s = 0x401;
sp->s_fval[WHITE][1].s = 0x401;
sp->s_fval[WHITE][2].s = 0x401;
sp->s_fval[WHITE][3].s = 0x401;
}
if (i > BSZ-4) { // directions 0, 1 are blocked
sp->s_flg |= BFLAG | (BFLAG << 1);
sp->s_fval[BLACK][0].s = MAXCOMBO;
sp->s_fval[BLACK][1].s = MAXCOMBO;
sp->s_fval[WHITE][0].s = MAXCOMBO;
sp->s_fval[WHITE][1].s = MAXCOMBO;
} else if (i == BSZ-4) { // if direction 1 is not blocked
sp->s_fval[BLACK][0].s = 0x500;
sp->s_fval[WHITE][0].s = 0x500;
if (!(sp->s_flg & (BFLAG << 1))) {
sp->s_fval[BLACK][1].s = 0x500;
sp->s_fval[WHITE][1].s = 0x500;
}
} else { // direction 3 is blocked
sp->s_fval[BLACK][0].s = 0x401;
sp->s_fval[WHITE][0].s = 0x401;
if (i < 5) {
sp->s_flg |= BFLAG << 3;
sp->s_fval[BLACK][3].s = MAXCOMBO;
sp->s_fval[WHITE][3].s = MAXCOMBO;
} else if (i == 5 && !(sp->s_flg & (BFLAG << 3))) {
sp->s_fval[BLACK][3].s = 0x500;
sp->s_fval[WHITE][3].s = 0x500;
}
}
// Allocate a frame structure for non blocked frames.
for (int r = 4; --r >= 0;) {
if (sp->s_flg & (BFLAG << r))
continue;
cbp->c_combo.s = sp->s_fval[BLACK][r].s;
cbp->c_vertex = sp - _board;
cbp->c_nframes = 1;
cbp->c_dir = r;
sp->s_frame[r] = cbp;
++cbp;
}
}
sp->s_occ = BORDER; // left & right border
sp->s_flg = BFLAGALL;
}
// mark the borders as such
for (int i = BSZ1; --i >= 0; ++sp) {
sp->s_occ = BORDER; // bottom border
sp->s_flg = BFLAGALL;
}
_sortframes[BLACK] = NULL;
_sortframes[WHITE] = NULL;
init_overlap();
}
static int align(EdStruct *xx0, int pos0, int len0,
EdStruct *xx1, int pos1, int len1)
{
char *ol0,*ol1, *cons0, *cons1;
int old_def_conf0 = xx0->default_conf_n;
int old_def_conf1 = xx1->default_conf_n;
OVERLAP *overlap;
int ierr;
char PAD_SYM = '.';
int *depad_to_pad0, *dp0, *depad_to_pad1, *dp1;
int *S, *res;
int off0 = 0, off1 = 0;
int left0 = 0, left1 = 0;
vfuncheader("Align contigs (join editor)");
/* Memory allocation */
ol0 = (char *) xmalloc(len0+1);
ol1 = (char *) xmalloc(len1+1);
cons0 = (char *) xmalloc(len0+1);
cons1 = (char *) xmalloc(len1+1);
dp0 = depad_to_pad0 = (int *)xmalloc((len0+1) * sizeof(int));
dp1 = depad_to_pad1 = (int *)xmalloc((len1+1) * sizeof(int));
/* Compute the consensus */
DBcalcConsensus(xx0,pos0,len0,ol0,NULL,BOTH_STRANDS);
DBcalcConsensus(xx1,pos1,len1,ol1,NULL,BOTH_STRANDS);
memcpy(cons0, ol0, len0+1);
memcpy(cons1, ol1, len1+1);
/* Strip the pads from the consensus */
depad_seq(ol0, &len0, depad_to_pad0);
depad_seq(ol1, &len1, depad_to_pad1);
if (NULL == (overlap = create_overlap())) return -1;
init_overlap (overlap, ol0, ol1, len0, len1);
if(-1 == (ierr = align_contigs (overlap))) {
xfree(ol0);
xfree(ol1);
destroy_overlap(overlap);
return -1;
}
/*
overlap->seq1_out[overlap->right+1] = 0;
overlap->seq2_out[overlap->right+1] = 0;
*/
S = res = rsalign2myers(overlap->seq1_out, strlen(overlap->seq1_out),
overlap->seq2_out, strlen(overlap->seq2_out),
PAD_SYM);
/* Clip left end */
if (*S != 0) {
/* Pad at start, so shift contigs */
if (*S < 0) {
left0 = -*S; /* used for display only */
depad_to_pad0 += -*S;
off0 = depad_to_pad0[0];
xx1->displayPos -= off0;
pos0 += off0;
len0 -= -*S;
} else {
left1 = *S; /* used for display only */
depad_to_pad1 += *S;
off1 = depad_to_pad1[0];
xx0->displayPos -= off1;
pos1 += off1;
len1 -= *S;
}
S++;
xx0->link->lockOffset = xx1->displayPos - xx0->displayPos;
}
/* Clip right end */
{
int pos0 = 0, pos1 = 0;
int *s = S;
while (pos0 < len0 && pos1 < len1) {
if (*s < 0) {
pos0 -= *s;
} else if (*s > 0) {
pos0 += *s;
} else {
pos0++;
pos1++;
}
s++;
}
if (*s < 0)
len0 += *s;
else if (*s > 0)
len1 -= *s;
}
/* Display the alignment. */
{
char *exp0, *exp1;
int exp_len0, exp_len1;
char name0[100];
char name1[100];
exp0 = (char *) xmalloc(len0+len1+1);
exp1 = (char *) xmalloc(len0+len1+1);
sprintf(name0, "%d", xx0->DBi->DB_contigNum);
sprintf(name1, "%d", xx1->DBi->DB_contigNum);
cexpand(ol0+left0, ol1+left1, len0, len1,
exp0, exp1, &exp_len0, &exp_len1,
ALIGN_J_SSH | ALIGN_J_PADS, S);
list_alignment(exp0, exp1, name0, name1, pos0, pos1, "");
xfree(exp0);
xfree(exp1);
}
/*************************************************************************/
/* Now actually make the edits, keeping track of old and new pads. */
openUndo(DBI(xx0));
openUndo(DBI(xx1));
xx0->default_conf_n = -1;
xx1->default_conf_n = -1;
{
int depad_pos0 = 0, depad_pos1 = 0;
int curr_pad0; /* Current padded position in seq 0 */
int curr_pad1; /* Current padded position in seq 1 */
int extra_pads; /* Difference between padded positions */
int last_pad0 = -1;
int last_pad1 = -1;
int inserted_bases0 = 0;
int inserted_bases1 = 0;
while (depad_pos0 < len0 && depad_pos1 < len1) {
if (*S < 0) {
depad_pos0 -= *S;
} else if (*S > 0) {
depad_pos1 += *S;
}
if (depad_pos0 >= len0 || depad_pos1 >= len1)
break;
curr_pad0 = depad_to_pad0[depad_pos0]-off0;
curr_pad1 = depad_to_pad1[depad_pos1]-off1;
extra_pads = (curr_pad1 - last_pad1) - (curr_pad0 - last_pad0);
if (extra_pads < 0) { /* Add to seq 0 */
add_pads(xx1, pos1 + curr_pad1 + inserted_bases1, -extra_pads);
inserted_bases1 -= extra_pads;
} else if (extra_pads > 0) { /* Add to seq 1 */
add_pads(xx0, pos0 + curr_pad0 + inserted_bases0, extra_pads);
inserted_bases0 += extra_pads;
}
last_pad0 = curr_pad0;
last_pad1 = curr_pad1;
if (*S == 0) {
depad_pos0++;
depad_pos1++;
}
S++;
}
}
xx0->default_conf_n = old_def_conf0;
xx1->default_conf_n = old_def_conf1;
/*************************************************************************/
closeUndo(xx1, DBI(xx1));
closeUndo(xx0, DBI(xx0));
xfree(res);
xx0->default_conf_n = old_def_conf0;
xx1->default_conf_n = old_def_conf1;
xfree(ol0);
xfree(ol1);
xfree(dp0);
xfree(dp1);
destroy_overlap(overlap);
return(0);
}
static int align(EdStruct *xx0, int pos0, int len0,
EdStruct *xx1, int pos1, int len1)
{
char *ol0,*ol1;
int old_def_conf0 = xx0->default_conf_n;
int old_def_conf1 = xx1->default_conf_n;
OVERLAP *overlap;
int ierr;
int left0, left1;
char name0[100];
char name1[100];
int i,pads;
char PAD_SYM = '.';
vfuncheader("Align contigs (join editor)");
/* Memory allocation */
ol0 = (char *) xmalloc(len0+1);
ol1 = (char *) xmalloc(len1+1);
/* Compute the consensus */
DBcalcConsensus(xx0,pos0,len0,ol0,NULL,BOTH_STRANDS);
DBcalcConsensus(xx1,pos1,len1,ol1,NULL,BOTH_STRANDS);
if (NULL == (overlap = create_overlap())) return -1;
init_overlap (overlap, ol0, ol1, len0, len1);
if(1 > (ierr = align_contigs (overlap))) {
xfree(ol0);
xfree(ol1);
destroy_overlap(overlap);
return -1;
}
/* Display the alignment. */
sprintf(name0, "#%d", xx0->DBi->DB[1].number);
sprintf(name1, "#%d", xx1->DBi->DB[1].number);
overlap->seq1_out[overlap->right+1] = 0;
overlap->seq2_out[overlap->right+1] = 0;
left0 = left1 = 0;
if(overlap->left1 == 0) left0 += overlap->left2;
if(overlap->left2 == 0) left1 += overlap->left1;
list_alignment(&overlap->seq1_out[overlap->left],
&overlap->seq2_out[overlap->left],
name0, name1, pos0+left0, pos1+left1, "");
xx1->displayPos -= left0;
xx0->displayPos -= left1;
xx0->link->lockOffset = xx1->displayPos - xx0->displayPos;
/* do the edits */
xx0->default_conf_n = -1;
xx1->default_conf_n = -1;
for(i=overlap->left,pads=0;i<=overlap->right;i++) {
if(overlap->seq1_out[i] != PAD_SYM) {
if(pads) {
add_pads(xx0, pos0-left1+i-pads, pads);
pads = 0;
}
}
else {
pads++;
}
}
if(pads) {
add_pads(xx0, pos0-left1+i-pads-1, pads);
}
for(i=overlap->left,pads=0;i<=overlap->right;i++) {
if(overlap->seq2_out[i] != PAD_SYM) {
if(pads) {
add_pads(xx1, pos1-left0+i-pads, pads);
pads = 0;
}
}
else {
pads++;
}
}
if(pads) {
add_pads(xx1, pos1-left0+i-pads-1, pads);
}
xx0->default_conf_n = old_def_conf0;
xx1->default_conf_n = old_def_conf1;
xfree(ol0);
xfree(ol1);
destroy_overlap(overlap);
return(0);
}
