void
NDalign::realignForward(bool verbose, bool displayAlign) {
Match_Node_t match;
match.Start = abgn(); // Begin position in a
match.Offset = bbgn(); // Begin position in b
match.Len = 0;
match.Next = 0; // Not used here
int32 aLo=0, aHi=0;
int32 bLo=0, bHi=0;
if (displayAlign)
fprintf(stderr, "NDalign::realignForward()--\n");
pedOverlapType olapType = _editDist->Extend_Alignment(&match, // Initial exact match, relative to start of string
_aStr, _aLen,
_bStr, _bLen,
aLo, aHi, // Output: Regions which the match extends
bLo, bHi);
aHi++; // Add one to the end point because Extend_Alignment returns the base-based coordinate.
bHi++;
// Is this a better overlap than what we have?
if (((score() < _editDist->score())) ||
((score() <= _editDist->score()) && (length() > ((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2))) {
if (displayAlign)
fprintf(stderr, "NDalign::realignForward()-- Save better alignment - OLD length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
_bestResult.save(aLo, aHi, bLo, bHi, _editDist->score(), olapType, _editDist->Left_Delta_Len, _editDist->Left_Delta);
display("NDalign::realignForward()-- ", false);
_bestResult.setErate(1.0 - (double)(_matches + _gapmatches) / (length() - _freegaps));
if (displayAlign)
fprintf(stderr, "NDalign::realignForward()-- Save better alignment - NEW length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
}
else if (displayAlign) {
fprintf(stderr, "NDalign::realignForward()-- Alignment no better - OLD length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
fprintf(stderr, "NDalign::realignForward()-- Alignment no better - NEW length %u erate %f score %u (%d-%d %d-%d)\n",
((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2, 0.0, _editDist->score(), aLo, aHi, bLo, bHi);
//display("NDalign::realignForward(NB)--", aLo, aHi, bLo, bHi, _editDist->Left_Delta, _editDist->Left_Delta_Len, true, false);
}
}
void cholesky (double **orig, double **chol, int tr, int dept)
{
int i, j, k;
FILE *error;
start:
for (i = 0; i < tr; i++) {
chol[i][i] = orig[i][i];
for (k = 0; k < i; k++)
chol[i][i] -= chol[k][i]*chol[k][i];
if (chol[i][i] <= 0) {
bend(orig, orig, tr);
error = fopen("./std.error.txt", "a");
fprintf(error, "\nERROR: non-positive definite matrix!\n");
dept++;
fprintf(error, "\nproblem from %d %f %d\n", i, chol[i][i], dept);
fclose(error);
goto start;
}
chol[i][i] = sqrt(chol[i][i]);
for (j = i+1; j < tr; j++) {
chol[i][j] = orig[i][j];
for (k = 0; k < i; k++)
chol[i][j] -= chol[k][i]*chol[k][j];
chol[i][j] /= chol[i][i];
chol[j][i] = chol[i][j];
}
}
}
forall_edges(e,G)
{
const BendString &bs1 = bend(e->adjSource());
const BendString &bs2 = bend(e->adjTarget());
if (bs1.size() != bs2.size()) {
error.sprintf(
"Size of corresponding bend strings at edge %d differ!",
e->index());
return false;
}
size_t i = 0, j = bs2.size()-1;
while(i < bs1.size()) {
if (bs1[i] != flip(bs2[j])) {
error.sprintf(
"Corresponding bend strings at edge %d not consistent!",
e->index());
return false;
}
++i; --j;
}
}
void mouseMove(int x, int y){
// this will only be true when the left button is down
if (xOrigin >= 0) {
// update deltaAngle
deltaAnglex = (x - xOrigin) * 0.0005f;
deltaAngley = (y - yOrigin) * 0.0001f;
// bend that shit
for (int i = 0; i < numballs; i++) {
balls[i].tempvelocity = balls[i].oldvelocity;
}
bend();
}
}
void Box::transformVertex(QVector3D v, float animationFrame)
{
switch (m_globalDefMode)
{
case Pinch:
pinch(v, 1.0f - animationFrame);
break;
case Mold:
mold(v, 1.0f - animationFrame);
break;
case Twist:
twist(v, animationFrame*360.0f);
break;
case Bend:
bend(v, animationFrame*90.0f);
break;
default:
glVertex3fv(&v[0]);
}
}
/* makeStraightEdge:
*
* FIX: handle ports on boundary?
*/
void
makeStraightEdge(graph_t * g, edge_t * e, int et, splineInfo* sinfo)
{
pointf dumb[4];
node_t *n = agtail(e);
node_t *head = aghead(e);
int e_cnt = ED_count(e);
int curved = (et == ET_CURVED);
pointf perp;
pointf del;
edge_t *e0;
int i, j, xstep, dx;
double l_perp;
pointf dumber[4];
pointf p, q;
p = dumb[1] = dumb[0] = add_pointf(ND_coord(n), ED_tail_port(e).p);
q = dumb[2] = dumb[3] = add_pointf(ND_coord(head), ED_head_port(e).p);
if ((e_cnt == 1) || Concentrate) {
if (curved) bend(dumb,get_centroid(g));
clip_and_install(e, aghead(e), dumb, 4, sinfo);
addEdgeLabels(g, e, p, q);
return;
}
e0 = e;
if (APPROXEQPT(dumb[0], dumb[3], MILLIPOINT)) {
/* degenerate case */
dumb[1] = dumb[0];
dumb[2] = dumb[3];
del.x = 0;
del.y = 0;
}
else {
perp.x = dumb[0].y - dumb[3].y;
perp.y = dumb[3].x - dumb[0].x;
l_perp = LEN(perp.x, perp.y);
xstep = GD_nodesep(g->root);
dx = xstep * (e_cnt - 1) / 2;
dumb[1].x = dumb[0].x + (dx * perp.x) / l_perp;
dumb[1].y = dumb[0].y + (dx * perp.y) / l_perp;
dumb[2].x = dumb[3].x + (dx * perp.x) / l_perp;
dumb[2].y = dumb[3].y + (dx * perp.y) / l_perp;
del.x = -xstep * perp.x / l_perp;
del.y = -xstep * perp.y / l_perp;
}
for (i = 0; i < e_cnt; i++) {
if (aghead(e0) == head) {
p = dumb[0];
q = dumb[3];
for (j = 0; j < 4; j++) {
dumber[j] = dumb[j];
}
} else {
p = dumb[3];
q = dumb[0];
for (j = 0; j < 4; j++) {
dumber[3 - j] = dumb[j];
}
}
if (et == ET_PLINE) {
Ppoint_t pts[4];
Ppolyline_t spl, line;
line.pn = 4;
line.ps = pts;
for (j=0; j < 4; j++) {
pts[j] = dumber[j];
}
make_polyline (line, &spl);
clip_and_install(e0, aghead(e0), spl.ps, spl.pn, sinfo);
}
else
clip_and_install(e0, aghead(e0), dumber, 4, sinfo);
addEdgeLabels(g, e0, p, q);
e0 = ED_to_virt(e0);
dumb[1].x += del.x;
dumb[1].y += del.y;
dumb[2].x += del.x;
dumb[2].y += del.y;
}
}
bool
NDalign::processHits(void) {
// If the first time here, set the hit iterator to zero, otherwise move to the next one.
// And then return if there are no more hits to iterate over.
if (_hitr == UINT32_MAX)
_hitr = 0;
else
_hitr++;
if (_hitr >= _hits.size())
return(false);
// While hits, process them.
//
// If a good hit is found, return, leaving hitr as is. The next time we enter this function,
// we'll increment hitr and process the next hit. If no good hit is found, we iterate the loop
// until a good one is found, or we run out of hits.
for (; _hitr < _hits.size(); _hitr++) {
Match_Node_t match;
match.Start = _hits[_hitr].aBgn; // Begin position in a
match.Offset = _hits[_hitr].bBgn; // Begin position in b
match.Len = _hits[_hitr].tLen; // tLen can include mismatches if alternate scoring is used!
match.Next = 0; // Not used here
#ifdef SEED_NON_OVERLAPPING
match.Offset = _merSize; // Really should track this in the hits, oh well.
#endif
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "\n");
fprintf(stderr, "NDalign::processHits()-- Extend_Alignment Astart %d Bstart %d length %d\n", match.Start, match.Offset, match.Len);
#endif
int32 aLo=0, aHi=0;
int32 bLo=0, bHi=0;
pedOverlapType olapType = _editDist->Extend_Alignment(&match, // Initial exact match, relative to start of string
_aStr, _aLen,
_bStr, _bLen,
aLo, aHi, // Output: Regions which the match extends
bLo, bHi);
aHi++; // Add one to the end point because Extend_Alignment returns the base-based coordinate.
bHi++;
// Is this a better overlap than what we have? Save it and update statistics.
if (((score() < _editDist->score())) ||
((score() <= _editDist->score()) && (length() > ((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2))) {
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "NDalign::processHits()-- Save better alignment - OLD length %u erate %f score %u (%d-%d %d-%d) ",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
#endif
_bestResult.save(aLo, aHi, bLo, bHi, _editDist->score(), olapType, _editDist->Left_Delta_Len, _editDist->Left_Delta);
display("NDalign::processHits()-- ", false);
_bestResult.setErate(1.0 - (double)(_matches + _gapmatches) / (length() - _freegaps));
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "NDalign::processHits()-- NEW length %u erate %f score %u (%d-%d %d-%d)\n",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
#endif
} else {
olapType = pedBothBranch;
#ifdef DEBUG_ALGORITHM
fprintf(stderr, "NDalign::processHits()-- DON'T save alignment - OLD length %u erate %f score %u (%d-%d %d-%d) ",
length(), erate(), score(), abgn(), aend(), bbgn(), bend());
fprintf(stderr, "NDalign::processHits()-- NEW length %u score %u coords %u-%u %u-%u\n",
((aHi - aLo) + (bHi - bLo) + _editDist->Left_Delta_Len) / 2,
_editDist->score(),
aLo, aHi, bLo, bHi);
#endif
}
// If a dovetail, we're done. Let the client figure out if the quality is good.
if (olapType == pedDovetail)
return(true);
} // Over all seeds.
// No more seeds to align. Did we save an alignment?
return(score() > 0);
}
std::shared_ptr<Model> Deserno2005ModelFactory::create() const {
auto model = std::make_shared<Model>(num_lipid * 3);
std::shared_ptr<FENEBondPotential> head_tail_bond(
new FENEBondPotential(
/* r0= */1.5*sigma,
/* k = */30*epsilon/sigma/sigma,
/* b = */0.95*sigma,
/* e = */epsilon));
for (std::size_t i(0); i < num_lipid; ++i)
head_tail_bond->add_bond(std::make_pair(i*3, i*3+1));
model->add_potential(head_tail_bond);
std::shared_ptr<FENEBondPotential> tail_tail_bond(
new FENEBondPotential(
/* r0= */1.5*sigma,
/* k = */30*epsilon/sigma/sigma,
/* b = */sigma,
/* e = */epsilon));
for (std::size_t i(0); i < num_lipid; ++i)
tail_tail_bond->add_bond(std::make_pair(i*3+1, i*3+2));
model->add_potential(tail_tail_bond);
std::shared_ptr<LowestOrderHarmonicBendPotential> bend(
new LowestOrderHarmonicBendPotential(
/* r0= */4*sigma,
/* k = */10*epsilon/sigma/sigma));
for (std::size_t i(0); i < num_lipid; ++i)
bend->add_pair(std::make_pair(i*3, i*3+2));
model->add_potential(bend);
std::shared_ptr<WeeksChandlerAndersonPotential> head_head_replusion(
new WeeksChandlerAndersonPotential(
/* s= */0.95*sigma,
/* e= */epsilon));
head_head_replusion->set_pair("LH", "LH");
model->add_potential(head_head_replusion);
std::shared_ptr<WeeksChandlerAndersonPotential> head_tail_replusion(
new WeeksChandlerAndersonPotential(
/* s= */0.95*sigma,
/* e= */epsilon));
head_tail_replusion->set_pair("LH", "LT");
model->add_potential(head_tail_replusion);
std::shared_ptr<WeeksChandlerAndersonPotential> tail_tail_replusion(
new WeeksChandlerAndersonPotential(
/* s= */sigma,
/* e= */epsilon));
tail_tail_replusion->set_pair("LT", "LT");
model->add_potential(tail_tail_replusion);
std::shared_ptr<TailsAttractionPotential> tails_attraction(
new TailsAttractionPotential(
/* r_c= */pow(2,1.0/6.0)*sigma,
/* w_c= */w_c,
/* e = */epsilon));
tails_attraction->set_pair("LT", "LT");
model->add_potential(tails_attraction);
return model;
}
void dogde()
{ int i,j,ran;
char ch,menu;
loading();
cleardevice();
setbkcolor(YELLOW);
setcolor(BLUE);
h:
outtextxy(100,100,"Press I to read instructions.");
outtextxy(100,200,"Press S to start the game.");
outtextxy(100,300,"Press E to exit.");
menu=getchar();
clrscr();
toupper(menu);
switch(menu)
{ case 'S' : break;
case 's' : break;
case 'I' : instructions();
goto h;
case 'i' : instructions();
goto h;
case 'E' : exit(0);
case 'e' : exit(0);
default : goto h;
}
setviewport(0,170,639,310,1);
start:
setbkcolor(YELLOW);
randomize();
ran=random(2);
if(ran==0)
{
for(i=0;i<639;i++)
{ draw_man();
setcolor(RED);
rectangle(635-i,120,639-i,140);
setcolor(BLACK);
rectangle(637-i,120,641-i,140);
man.top_y=90;
man.top_x=55;
man.bottom_x=55;
man.bottom_y=140;
obstacle.x=635-i;
obstacle.y=120;
if(kbhit())
{ ch=getch();
if(ch=='y'||ch=='Y')
{ i=jump(i,ran);
draw_man();
if(man.bottom_x>obstacle.x)
{ score++;
goto start; }
else if(man.bottom_y >=obstacle.y && man.bottom_x==obstacle.x)
{
gameover();
}
}
else if(ch=='h'||ch=='H')
{ i=bend(i,ran);
draw_man();
if(man.bottom_x>obstacle.x)
{ score++;
goto start; }
else if(man.bottom_y >=obstacle.y && man.bottom_x==obstacle.x)
{
gameover();
}
}
}
delay(10);
}
}
else if(ran==1)
{
for(i=0;i<639;i++)
{ draw_man();
setcolor(RED);
rectangle(635-i,20,639-i,80);
setcolor(BLACK);
rectangle(637-i,20,641-i,80);
obstacle.x=635-i;
obstacle.y=60;
if(kbhit())
{ ch=getch();
if(ch=='y'||ch=='Y')
{ i=jump(i,ran);
draw_man();
if(man.bottom_x>obstacle.x)
{ score++;
goto start; }
else if(man.top_y<=obstacle.y && man.bottom_x==obstacle.x)
{
gameover();
}
}
else if(ch=='h'||ch=='H')
{ i=bend(i,ran);
draw_man();
if(man.bottom_x>obstacle.x)
{ score++;
goto start; }
else if(man.bottom_y >=obstacle.y && man.bottom_x==obstacle.x)
{
gameover();
}
}
}
delay(10);
}
}
gameover();
closegraph();
}
