cMobile::~cMobile() {
freeSequence();
if (this == Player) {
Player = 0; // Reset player to null -> important
}
}
void scanFile(FILE *fp, Args *args) {
Sequence *seq = NULL;
char *oldChr;
int start, end;
FILE *snp;
oldChr = (char *)emalloc(sizeof(char));
oldChr[0] = '\0';
while (tabGetLine(fp) != NULL) {
/* read chromosome, start, and end of hotspot from line */
if (tabField(0)[0] == '#')
continue;
if (strcmp(oldChr, hotSpotGetChr()) != 0) {
if (seq)
freeSequence(seq);
seq = hotSpotSeq(args);
free(oldChr);
oldChr = estrdup(hotSpotGetChr());
}
start = atoi(tabField(START_FIELD));
end = atoi(tabField(END_FIELD));
if (args->r) {
/* reverse primers are downstream of hotspot */
start = end;
end += args->f;
snp = hotSpotSnp(args, start, end);
if(args->u)
reversePuniv(args, seq, snp, start, end);
else
reverseP(args, seq, snp);
} else {
/* forward primers are upstream of hotspot */
end = start;
start -= args->f;
snp = hotSpotSnp(args, start, end);
if(args->u)
forwardPuniv(args, seq, snp, start, end);
else
forwardP(args, seq, snp);
}
pclose(snp);
}
freeSequence(seq);
free(oldChr);
}
void cMobile::playAction(unsigned char action, unsigned int duration) {
if (currentAction_ != action) {
freeSequence(); // Free old sequence if the actions dont match
}
// Set the action and the duration
currentAction_ = action;
currentActionEnd_ = Utilities::getTicks() + duration;
}
/* deallocate memory for an array of sequence */
void freeSequenceArray(Int64 n, Sequence *seqArray[]) {
Int64 i;
for (i = 0; i < n; i++) {
if (seqArray[i]) {
freeSequence(seqArray[i]);
}
}
free(seqArray);
}
void cMobile::setWarmode(bool data) {
if (data != warmode) {
warmode = data;
if (currentActionEnd_ == 0) {
freeSequence();
currentAction_ = getIdleAction();
}
Network->emitWarmodeChanged(data);
}
}
void LKH::LKHAlg::freeAll()
{
freeERXT();
freeGain23();
freeSequence();
freeCreateDelaunay();
freeCreateQuadrant();
freeGreedyTour();
freePatchCycle();
freeReadPenalties();
}
cMobile::~cMobile() {
deleting = true;
freeSequence();
if (this == Player) {
Player = 0; // Reset player to null -> important
}
clearEquipment();
delete status_;
}
void cMobile::draw(int cellx, int celly, int leftClip, int topClip, int rightClip, int bottomClip) {
//return; // Don't draw yet
// See if the current action expired
if (currentActionEnd_ != 0 && currentActionEnd_ < Utilities::getTicks()) {
freeSequence(); // Free current surface
currentActionEnd_ = 0; // Reset end time
currentAction_ = getIdleAction();
}
// Refresh the sequence
if (!sequence_) {
refreshSequence();
}
// Modify cellx/celly based on the smooth move settings
// Smooth move handling.
if (smoothMoveEnd != 0) {
int moveProgress = smoothMoveTime - (smoothMoveEnd - Utilities::getTicks());
if (moveProgress < 0 || moveProgress >= (int)smoothMoveTime) {
smoothMoveEnd = 0;
} else {
if (moveProgress <= 0) {
cellx += drawxoffset;
celly += drawyoffset;
frame = 0;
} else {
float factor = 1.0f - (float)moveProgress / (float)smoothMoveTime;
cellx += (int)(factor * (float)drawxoffset);
celly += (int)(factor * (float)drawyoffset);
if (sequence_) {
frame = (int)(sequence_->frameCount() * factor);
}
}
}
}
// Draw
if (sequence_) {
// Skip to next frame
if (smoothMoveEnd == 0 && nextFrame < Utilities::getTicks()) {
if (++frame >= sequence_->frameCount()) {
frame = 0;
}
nextFrame = Utilities::getTicks() + getFrameDelay();
}
// The anims facing right are generated by flipping the ones facing left
bool flip = (direction_ > 0 && direction_ < 4);
sequence_->draw(frame, cellx, celly, flip);
}
}
/* deallocates memory for a seqArray */
void freeSequenceUnion(SequenceUnion *seqUnion, Int64 n) {
int i;
freeSequence(seqUnion->seqUnion);
free(seqUnion->seqBorders);
//for (i = 0; i < seqUnion->numOfSubjects + 1; i ++) {
for (i = 0; i < n; i ++) {
free(seqUnion->bordersWithinSeq[i]);
}
free(seqUnion->bordersWithinSeq);
free(seqUnion->gc);
free(seqUnion);
}
/* prepareSeq: prepares sequence string for analysis by shustring-type programs.
* Does the following: 1) set all residues to upper case
* 2) generate reverse complement
* 3) concatenate reverse complement to end of forward strand
* e.g. if the string of the original seq. is ACCGZ\0, (Z for the border)
* then the new one which includes the reversed complement seq. looks like this: ACCGZCGGTZ\0
*
*/
void prepareSeq(Sequence *sequence){
Sequence *rstrand;
Int64 i, j;
char *nuc = "TCAGtcag";
strtoupper(sequence->seq);
/* take care of reverse strand */
rstrand = revcomp(sequence); /* reverse and complement a sequence */
rstrand->headers = (char **)emalloc(sizeof(char *));
rstrand->headers[0] = (char *)emalloc(sizeof(char));
rstrand->borders = (Int64 *)emalloc(sizeof(Int64));
rstrand->freqTab = NULL;
rstrand->numSeq = 1;
sequence->seq[sequence->len] = '\0';
sequence->len += sequence->len; /* new seq. length = 2 x original size */
sequence->seq = (char *)erealloc(sequence->seq,(size_t)(sequence->len+1)*sizeof(char));
/* number of borders = 2 x original size */
sequence->borders = (Int64 *)erealloc(sequence->borders, 2*(size_t)sequence->numSeq * sizeof(Int64));
/* adjust the border values */
for(i=1;i<sequence->numSeq;i++){
/* seq. looks like this: F1 F2 .. Fn Rn .. R2 R1 */
sequence->borders[2*sequence->numSeq-i-1] = sequence->len - sequence->borders[i-1] - 2;
}
sequence->borders[2*sequence->numSeq-1] = sequence->len - 1;
/* move first border of reverted sequences to the end */
rstrand->seq++; /* since the last border of the original seq is the first char of the reversed seq */
//strncat(sequence->seq,rstrand->seq,(size_t)sequence->len); ??
strncat(sequence->seq,rstrand->seq,(size_t)sequence->len / 2);
rstrand->seq--; /* return the pointer */
sequence->seq[sequence->len-1] = BORDER;
sequence->seq[sequence->len] = '\0';
freeSequence(rstrand);
sequence->numNuc = 0;
for(i = 0; i < 8; i++) {
//sequence->numNuc += sequence->freqTab[(int)nuc[i]];
for (j = 0; j < sequence->numNuc; j ++) {
sequence->numNuc += sequence->freqTab[j][(Int64)nuc[i]];
sequence->freqTab[j][(Int64)nuc[i]] *= 2; /* fwd and rev strand */
}
}
sequence->numNuc *= 2;
sequence->numSbjctNuc *= 2;
}
void cMobile::draw(int cellx, int celly, int leftClip, int topClip, int rightClip, int bottomClip) {
// Save the original cellx, celly for the greyed out stuff
int orgCellX = cellx;
int orgCellY = celly;
static int cellXOffset = 0;
static int cellYOffset = 0;
if (Config->gameHideMobiles()) {
return;
}
// Test for smoother player movement
if (this == Player) {
cellx = WorldView->x() + WorldView->width() / 2;
celly = WorldView->y() + WorldView->height() / 2;
}
cellx += cellXOffset;
celly += cellYOffset;
// See if the current action expired
if (currentActionEnd_ != 0 && currentActionEnd_ < Utilities::getTicks()) {
// Don't cancel the movement action while we're still moving -or- have movement requests left
if (this != Player || ((!WorldView->isMoving() || WorldView->isMovementBlocked()) && (!UoSocket || UoSocket->sequenceQueueLength() == 0))) {
freeSequence(); // Free current surface
currentActionEnd_ = 0; // Reset end time
currentAction_ = getIdleAction();
}
}
// Refresh the sequence
if (!sequence_) {
refreshSequence();
}
float alpha = 1.0f;
// Modify cellx/celly based on the smooth move settings
// Smooth move handling.
if (smoothMoveEnd != 0) {
int moveProgress = smoothMoveTime - (smoothMoveEnd - Utilities::getTicks());
if (moveProgress < 0 || moveProgress >= (int)smoothMoveTime) {
smoothMoveEnd = 0;
World->removeEntity(this);
World->addEntity(this);
} else if (this != Player) {
if (moveProgress <= 0) {
cellx += drawxoffset;
celly += drawyoffset;
} else {
float factor = 1.0f - (float)moveProgress / (float)smoothMoveTime;
cellx += (int)(factor * (float)drawxoffset);
celly += (int)(factor * (float)drawyoffset);
}
}
}
static bool inGreyDraw = false;
static bool inBlurDraw = false;
if (isHidden()) {
glPushAttrib(GL_ENABLE_BIT);
glEnable(GL_ALPHA_TEST); // Make sure that transparent pixels wont touch our stencil buffer
glAlphaFunc(GL_GREATER, 0.0f);
glEnable(GL_STENCIL_TEST); // Enable per-pixel stencil testing
glStencilFunc(GL_EQUAL, 1, 1); // Draw if stencil buffer is not zero
glStencilOp(GL_KEEP, GL_KEEP, GL_ZERO);
if (!inGreyDraw) {
glClearStencil(1);
glClear(GL_STENCIL_BUFFER_BIT);
}
static uint nextPeak = 0;
static uint lastPeak = 0;
static bool peakDirection = false;
uint time = Utilities::getTicks();
if (time >= nextPeak) {
lastPeak = Utilities::getTicks();
nextPeak = lastPeak + 1500 + Random->randInt(1000);
peakDirection = !peakDirection;
}
alpha = (nextPeak - Utilities::getTicks()) / (float)(nextPeak - lastPeak);
if (peakDirection) {
alpha = 1.0f - alpha;
}
if (inGreyDraw) {
if (inBlurDraw) {
alpha *= 0.5f;
} else {
alpha *= 0.8f;
}
} else {
GLWidget->enableGrayShader();
alpha = 0.8 * (1.0f - alpha); // Invert alpha value
}
}
// Draw
if (sequence_) {
// Only advance to the next frame if we're not beyond the end of this action
if (currentActionEnd_ != 0 && currentActionEnd_ >= Utilities::getTicks()) {
// Skip to next frame
if (nextFrame < Utilities::getTicks()) {
if (++frame >= sequence_->frameCount()) {
frame = 0;
}
nextFrame = Utilities::getTicks() + getFrameDelay();
}
}
// The anims facing right are generated by flipping the ones facing left
bool flip = (direction_ >= 0 && direction_ < 4);
// Mounts come always first
if (!isHidden()) {
if ((bodyType() == HUMAN || bodyType() == EQUIPMENT) && equipment[LAYER_MOUNT] && equipmentSequences[LAYER_MOUNT]) {
// Only advance to the next frame if we're not beyond the end of this action
if (currentActionEnd_ != 0 && currentActionEnd_ >= Utilities::getTicks()) {
// Skip to next frame
if (nextMountFrame < Utilities::getTicks()) {
if (++mountFrame >= equipmentSequences[LAYER_MOUNT]->frameCount()) {
mountFrame = 0;
}
nextMountFrame = Utilities::getTicks() + getMountFrameDelay();
}
}
mountFrame = frame; // Until something better is found
equipmentSequences[LAYER_MOUNT]->draw(mountFrame, cellx, celly, flip, alpha);
}
sequence_->draw(frame, cellx, celly, flip, alpha);
}
// Draw the equipment
if (bodyType() == HUMAN || bodyType() == EQUIPMENT) {
// Reverse the draw order if hidden
if (isHidden()) {
uint count = 0;
const int *order = drawOrder[direction_ % 8];
while (order[count] != -1) {
count++;
}
for (int i = count - 1; i >= 0; --i) {
enLayer layer = (enLayer)order[i];
if (layer < LAYER_VISIBLECOUNT && equipmentSequences[layer]) {
// Oh great OSI... Another exception from the rule *sigh*
// Don't draw Hair if we're wearing a gm robe
if (layer != LAYER_HAIR || !equipmentSequences[LAYER_OUTERTORSO] || equipmentSequences[LAYER_OUTERTORSO]->body() != 0x3db) {
equipmentSequences[layer]->draw(frame, cellx, celly, flip, alpha);
}
}
}
} else {
const int *order = drawOrder[direction_ % 8];
while (*order != -1) {
enLayer layer = (enLayer)*order;
if (layer < LAYER_VISIBLECOUNT && equipmentSequences[layer]) {
// Oh great OSI... Another exception from the rule *sigh*
// Don't draw Hair if we're wearing a gm robe
if (layer != LAYER_HAIR || !equipmentSequences[LAYER_OUTERTORSO] || equipmentSequences[LAYER_OUTERTORSO]->body() != 0x3db) {
equipmentSequences[layer]->draw(frame, cellx, celly, flip, alpha);
}
}
++order; // Next layer
}
}
}
// If we're hidden, mount+body come last
if (isHidden()) {
sequence_->draw(frame, cellx, celly, flip, alpha);
if ((bodyType() == HUMAN || bodyType() == EQUIPMENT) && equipment[LAYER_MOUNT] && equipmentSequences[LAYER_MOUNT]) {
// Only advance to the next frame if we're not beyond the end of this action
if (currentActionEnd_ != 0 && currentActionEnd_ >= Utilities::getTicks()) {
// Skip to next frame
if (nextMountFrame < Utilities::getTicks()) {
if (++mountFrame >= equipmentSequences[LAYER_MOUNT]->frameCount()) {
mountFrame = 0;
}
nextMountFrame = Utilities::getTicks() + getMountFrameDelay();
}
}
mountFrame = frame; // Until something better is found
equipmentSequences[LAYER_MOUNT]->draw(mountFrame, cellx, celly, flip, alpha);
}
}
}
if (isHidden()) {
glPopAttrib();
if (!inGreyDraw) {
GLWidget->disableGrayShader();
}
}
drawx_ = cellx;
drawy_ = celly;
if (isHidden() && !inGreyDraw) {
glClearStencil(1);
glClear(GL_STENCIL_BUFFER_BIT);
inGreyDraw = true;
inBlurDraw = true;
cellXOffset = 1;
draw(orgCellX, orgCellY, leftClip, topClip, rightClip, bottomClip);
cellXOffset = -1;
draw(orgCellX, orgCellY, leftClip, topClip, rightClip, bottomClip);
cellXOffset = 0;
cellYOffset = 1;
draw(orgCellX, orgCellY, leftClip, topClip, rightClip, bottomClip);
cellYOffset = -1;
draw(orgCellX, orgCellY, leftClip, topClip, rightClip, bottomClip);
cellYOffset = 0;
inBlurDraw = false;
draw(orgCellX, orgCellY, leftClip, topClip, rightClip, bottomClip);
inGreyDraw = false;
}
}