Esempio n. 1
0
cMobile::~cMobile() {
	freeSequence();

	if (this == Player) {
		Player = 0; // Reset player to null -> important
	}
}
Esempio n. 2
0
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);
}
Esempio n. 3
0
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;
}
Esempio n. 4
0
/* 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);
}
Esempio n. 5
0
void cMobile::setWarmode(bool data) {
	if (data != warmode) {
		warmode = data;
		if (currentActionEnd_ == 0) {
			freeSequence();
			currentAction_ = getIdleAction();
		}
		Network->emitWarmodeChanged(data);
	}
}
Esempio n. 6
0
void LKH::LKHAlg::freeAll()
{
	freeERXT();
	freeGain23();
	freeSequence();
	freeCreateDelaunay();
	freeCreateQuadrant();
	freeGreedyTour();
	freePatchCycle();
	freeReadPenalties();
}
Esempio n. 7
0
cMobile::~cMobile() {
	deleting = true;
	freeSequence();

	if (this == Player) {
		Player = 0; // Reset player to null -> important
	}

	clearEquipment();
	delete status_;
}
Esempio n. 8
0
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);
	}
}
Esempio n. 9
0
/* 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);
}
Esempio n. 10
0
/* 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;
}
Esempio n. 11
0
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;
	}
}