Esempio n. 1
0
ShowImageWindow::ShowImageWindow(const entry_ref *ref,
	const BMessenger& trackerMessenger)
	:
	BWindow(BRect(5, 24, 250, 100), "", B_DOCUMENT_WINDOW, 0),
	fSavePanel(NULL),
	fBar(NULL),
	fOpenMenu(NULL),
	fBrowseMenu(NULL),
	fGoToPageMenu(NULL),
	fSlideShowDelay(NULL),
	fImageView(NULL),
	fStatusView(NULL),
	fModified(false),
	fFullScreen(false),
	fShowCaption(true),
	fPrintSettings(NULL),
	fResizerWindowMessenger(NULL),
	fResizeItem(NULL),
	fHeight(0),
	fWidth(0)
{
	_LoadSettings();

	// create menu bar
	fBar = new BMenuBar(BRect(0, 0, Bounds().right, 1), "menu_bar");
	AddMenus(fBar);
	AddChild(fBar);

	BRect viewFrame = Bounds();
	viewFrame.top = fBar->Bounds().Height() + 1;
	viewFrame.right -= B_V_SCROLL_BAR_WIDTH;
	viewFrame.bottom -= B_H_SCROLL_BAR_HEIGHT;

	// create the image view
	fImageView = new ShowImageView(viewFrame, "image_view", B_FOLLOW_ALL,
		B_WILL_DRAW | B_FRAME_EVENTS | B_FULL_UPDATE_ON_RESIZE | B_PULSE_NEEDED);
	// wrap a scroll view around the view
	BScrollView *scrollView = new BScrollView("image_scroller", fImageView,
		B_FOLLOW_ALL, 0, false, false, B_PLAIN_BORDER);
	AddChild(scrollView);

	const int32 kstatusWidth = 190;
	BRect rect;
	rect = Bounds();
	rect.top	= viewFrame.bottom + 1;
	rect.left 	= viewFrame.left + kstatusWidth;
	rect.right	= viewFrame.right + 1;
	rect.bottom += 1;
	BScrollBar *horizontalScrollBar = new BScrollBar(rect, "hscroll",
		fImageView, 0, 150, B_HORIZONTAL);
	AddChild(horizontalScrollBar);

	rect.left = 0;
	rect.right = kstatusWidth - 1;
	rect.bottom -= 1;
	fStatusView = new ShowImageStatusView(rect, "status_view", B_FOLLOW_BOTTOM,
		B_WILL_DRAW);
	AddChild(fStatusView);

	rect = Bounds();
	rect.top	= viewFrame.top - 1;
	rect.left	= viewFrame.right + 1;
	rect.bottom	= viewFrame.bottom + 1;
	rect.right	+= 1;
	BScrollBar *verticalScrollBar = new BScrollBar(rect, "vscroll", fImageView,
		0, 150, B_VERTICAL);
	AddChild(verticalScrollBar);

	SetSizeLimits(250, 100000, 100, 100000);

	// finish creating the window
	fImageView->SetImage(ref);
	fImageView->SetTrackerMessenger(trackerMessenger);

	if (InitCheck() != B_OK) {
		BAlert* alert;
		alert = new BAlert("ShowImage",
			"Could not load image! Either the file or an image translator for "
			"it does not exist.", "OK", NULL, NULL, B_WIDTH_AS_USUAL, B_INFO_ALERT);
		alert->Go();

		// quit if file could not be opened
		Quit();
		return;
	}

	// add View menu here so it can access ShowImageView methods
	BMenu* menu = new BMenu("View");
	_BuildViewMenu(menu, false);
	fBar->AddItem(menu);
	_MarkMenuItem(fBar, MSG_DITHER_IMAGE, fImageView->GetDither());
	UpdateTitle();

	SetPulseRate(100000);
		// every 1/10 second; ShowImageView needs it for marching ants

	WindowRedimension(fImageView->GetBitmap());
	fImageView->MakeFocus(true); // to receive KeyDown messages
	Show();

	// Tell application object to query the clipboard
	// and tell this window if it contains interesting data or not
	be_app_messenger.SendMessage(B_CLIPBOARD_CHANGED);
}
Esempio n. 2
0
void DoMuscle(CompositeVect*CVLocation)
	{
	SetOutputFileName(g_pstrOutFileName);
	SetInputFileName(g_pstrInFileName);

	SetMaxIters(g_uMaxIters);
	SetSeqWeightMethod(g_SeqWeight1);

	TextFile fileIn(g_pstrInFileName);
	SeqVect v;
	v.FromFASTAFile(fileIn);
	const unsigned uSeqCount = v.Length();

	if (0 == uSeqCount)
		Quit("No sequences in input file");

	ALPHA Alpha = ALPHA_Undefined;
	switch (g_SeqType)
		{
	case SEQTYPE_Auto:
		Alpha = v.GuessAlpha();
		break;

	case SEQTYPE_Protein:
		Alpha = ALPHA_Amino;
		break;

	case SEQTYPE_DNA:
		Alpha = ALPHA_DNA;
		break;

	case SEQTYPE_RNA:
		Alpha = ALPHA_RNA;
		break;

	default:
		Quit("Invalid seq type");
		}
	SetAlpha(Alpha);
	v.FixAlpha();

	PTR_SCOREMATRIX UserMatrix = 0;
	if (0 != g_pstrMatrixFileName)
		{
		const char *FileName = g_pstrMatrixFileName;
		const char *Path = getenv("MUSCLE_MXPATH");
		if (Path != 0)
			{
			size_t n = strlen(Path) + 1 + strlen(FileName) + 1;
			char *NewFileName = new char[n];
			sprintf(NewFileName, "%s/%s", Path, FileName);
			FileName = NewFileName;
			}
		TextFile File(FileName);
		UserMatrix = ReadMx(File);
		g_Alpha = ALPHA_Amino;
		g_PPScore = PPSCORE_SP;
		}

	SetPPScore();

	if (0 != UserMatrix)
		g_ptrScoreMatrix = UserMatrix;

	unsigned uMaxL = 0;
	unsigned uTotL = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		unsigned L = v.GetSeq(uSeqIndex).Length();
		uTotL += L;
		if (L > uMaxL)
			uMaxL = L;
		}

	SetIter(1);
	g_bDiags = g_bDiags1;
	SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);

	SetMuscleSeqVect(v);

	MSA::SetIdCount(uSeqCount);

// Initialize sequence ids.
// From this point on, ids must somehow propogate from here.
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		v.SetSeqId(uSeqIndex, uSeqIndex);

	if (0 == uSeqCount)
		Quit("Input file '%s' has no sequences", g_pstrInFileName);
	if (1 == uSeqCount)
		{
		TextFile fileOut(g_pstrOutFileName, true);
		v.ToFile(fileOut);
		return;
		}

	if (uSeqCount > 1)
		MHackStart(v);

// First iteration
	Tree GuideTree;
	if (0 != g_pstrUseTreeFileName)
	{
	// Discourage users...
		if (!g_bUseTreeNoWarn)
			fprintf(stderr, "%s", g_strUseTreeWarning);

	// Read tree from file
		TextFile TreeFile(g_pstrUseTreeFileName);
		GuideTree.FromFile(TreeFile);

	// Make sure tree is rooted
		if (!GuideTree.IsRooted())
			Quit("User tree must be rooted");

		if (GuideTree.GetLeafCount() != uSeqCount)
			Quit("User tree does not match input sequences");

		const unsigned uNodeCount = GuideTree.GetNodeCount();
		for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
			{
			if (!GuideTree.IsLeaf(uNodeIndex))
				continue;
			const char *LeafName = GuideTree.GetLeafName(uNodeIndex);
			unsigned uSeqIndex;
			bool SeqFound = v.FindName(LeafName, &uSeqIndex);
			if (!SeqFound)
				Quit("Label %s in tree does not match sequences", LeafName);
			unsigned uId = v.GetSeqIdFromName(LeafName);
			GuideTree.SetLeafId(uNodeIndex, uId);
			}
		}
	else
		TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1,
		  g_pstrDistMxFileName1);

	const char *Tree1 = ValueOpt("Tree1");
	if (0 != Tree1)
		{
		TextFile f(Tree1, true);
		GuideTree.ToFile(f);
		if (g_bClusterOnly)
			return;
		}

	SetMuscleTree(GuideTree);
	ValidateMuscleIds(GuideTree);

	MSA msa;
	msa.SetCompositeVector(CVLocation);
	ProgNode *ProgNodes = 0;
	if (g_bLow)
		ProgNodes = ProgressiveAlignE(v, GuideTree, msa);
	else
		ProgressiveAlign(v, GuideTree, msa);
	SetCurrentAlignment(msa);

	if (0 != g_pstrComputeWeightsFileName)
		{
		extern void OutWeights(const char *FileName, const MSA &msa);
		SetMSAWeightsMuscle(msa);
		OutWeights(g_pstrComputeWeightsFileName, msa);
		return;
		}

	ValidateMuscleIds(msa);

	if (1 == g_uMaxIters || 2 == uSeqCount)
		{
		//TextFile fileOut(g_pstrOutFileName, true);
		//MHackEnd(msa);
		//msa.ToFile(fileOut);
		MuscleOutput(msa);
		return;
		}

	if (0 == g_pstrUseTreeFileName)
		{
		g_bDiags = g_bDiags2;
		SetIter(2);

		if (g_bLow)
			{
			if (0 != g_uMaxTreeRefineIters)
				RefineTreeE(msa, v, GuideTree, ProgNodes);
			}
		else
			RefineTree(msa, GuideTree);

		const char *Tree2 = ValueOpt("Tree2");
		if (0 != Tree2)
			{
			TextFile f(Tree2, true);
			GuideTree.ToFile(f);
			}
		}

	SetSeqWeightMethod(g_SeqWeight2);
	SetMuscleTree(GuideTree);

	if (g_bAnchors)
		RefineVert(msa, GuideTree, g_uMaxIters - 2);
	else
		RefineHoriz(msa, GuideTree, g_uMaxIters - 2, false, false);

#if	0
// Refining by subfamilies is disabled as it didn't give better
// results. I tried doing this before and after RefineHoriz.
// Should get back to this as it seems like this should work.
	RefineSubfams(msa, GuideTree, g_uMaxIters - 2);
#endif

	ValidateMuscleIds(msa);
	ValidateMuscleIds(GuideTree);

	//TextFile fileOut(g_pstrOutFileName, true);
	//MHackEnd(msa);
	//msa.ToFile(fileOut);
	MuscleOutput(msa);
	}
void C4Application::GameTick()
{
	// Exec depending on game state
	switch (AppState)
	{
	case C4AS_None:
		assert(AppState != C4AS_None);
		break;
	case C4AS_Quit:
		// Do nothing, the main loop will exit soon
		break;
	case C4AS_PreInit:
		if (!PreInit()) Quit();
		break;
	case C4AS_Startup:
		SoundSystem.Execute();
		MusicSystem.Execute();
		// wait for the user to start a game
		break;
	case C4AS_StartGame:
		// immediate progress to next state; OpenGame will enter HandleMessage-loops in startup and lobby!
		C4Startup::CloseStartup();
		AppState = C4AS_Game;
		// first-time game initialization
		if (!Game.Init())
		{
			// set error flag (unless this was a lobby user abort)
			if (!C4GameLobby::UserAbort)
				Game.fQuitWithError = true;
			// no start: Regular QuitGame; this may reset the engine to startup mode if desired
			QuitGame();
			break;
		}
		if(Config.Graphics.Windowed == 2 && FullScreenMode())
			Application.SetVideoMode(GetConfigWidth(), GetConfigHeight(), Config.Graphics.BitDepth, Config.Graphics.RefreshRate, Config.Graphics.Monitor, true);
		break;
	case C4AS_AfterGame:
		// stop game
		Game.Clear();
		if(Config.Graphics.Windowed == 2 && !NextMission && !isEditor)
			Application.SetVideoMode(GetConfigWidth(), GetConfigHeight(), Config.Graphics.BitDepth, Config.Graphics.RefreshRate, Config.Graphics.Monitor, false);
		AppState = C4AS_PreInit;
		// if a next mission is desired, set to start it
		if (NextMission)
		{
			Game.SetScenarioFilename(NextMission.getData());
			Game.fLobby = Game.NetworkActive;
			Game.fObserve = false;
			NextMission.Clear();
		}
		break;
	case C4AS_Game:
		// Game
		if (Game.IsRunning)
			Game.Execute();
		// Sound
		SoundSystem.Execute();
		MusicSystem.Execute();
		// Gamepad
		if (pGamePadControl) pGamePadControl->Execute();
		break;
	}
}
Esempio n. 4
0
int DebugKeys()
{
	boolean esc;
	int level;

	if (IN_KeyDown(sc_C))		// C = count objects
	{
		CountObjects();
		return 1;
	}

	if (IN_KeyDown(sc_E))		// E = quit level
	{
		playstate = ex_completed;
//		gamestate.mapon++;
	}

	if (IN_KeyDown(sc_F))		// F = facing spot
	{
		CenterWindow (14,4);
		US_Print ("X:");
		US_PrintUnsigned (player->x);
		US_Print ("\nY:");
		US_PrintUnsigned (player->y);
		US_Print ("\nA:");
		US_PrintUnsigned (player->angle);
		VW_UpdateScreen();
		IN_Ack();
		return 1;
	}

	if (IN_KeyDown(sc_G))		// G = god mode
	{
		CenterWindow (12,2);
		if (godmode)
		  US_PrintCentered ("God mode OFF");
		else
		  US_PrintCentered ("God mode ON");
		VW_UpdateScreen();
		IN_Ack();
		godmode ^= 1;
		return 1;
	}
	if (IN_KeyDown(sc_H))		// H = hurt self
	{
		IN_ClearKeysDown ();
		TakeDamage (16,NULL);
	}
	else if (IN_KeyDown(sc_I))			// I = item cheat
	{
		CenterWindow (12,3);
		US_PrintCentered ("Free items!");
		VW_UpdateScreen();
		GivePoints(100000);
		HealSelf(99);
		if (gamestate.bestweapon<wp_chaingun)
			GiveWeapon (gamestate.bestweapon+1);
		gamestate.ammo += 50;
		if (gamestate.ammo > 99)
			gamestate.ammo = 99;
		DrawAmmo ();
		IN_Ack ();
		return 1;
	}
	else if (IN_KeyDown(sc_N))			// N = no clip
	{
		noclip^=1;
		CenterWindow (18,3);
		if (noclip)
			US_PrintCentered ("No clipping ON");
		else
			US_PrintCentered ("No clipping OFF");
		VW_UpdateScreen();
		IN_Ack ();
		return 1;
	}
	else if (IN_KeyDown(sc_P))			// P = pause with no screen disruptioon
	{
		PicturePause ();
		return 1;
	}
	else if (IN_KeyDown(sc_Q))			// Q = fast quit
		Quit(NULL);
	else if (IN_KeyDown(sc_S))			// S = slow motion
	{
		singlestep^=1;
		CenterWindow (18,3);
		if (singlestep)
			US_PrintCentered ("Slow motion ON");
		else
			US_PrintCentered ("Slow motion OFF");
		VW_UpdateScreen();
		IN_Ack ();
		return 1;
	}
	else if (IN_KeyDown(sc_T))			// T = shape test
	{
		ShapeTest();
		return 1;
	}
	else if (IN_KeyDown(sc_W))			// W = warp to level
	{
		CenterWindow(26,3);
		PrintY+=6;
#ifndef SPEAR
		US_Print("  Warp to which level(1-10):");
#elif defined(SPEARDEMO)
		US_Print("  Warp to which level(1-2):");
#else
		US_Print("  Warp to which level(1-21):");
#endif
		VW_UpdateScreen();
		esc = !US_LineInput (px,py,str,NULL,true,2,0);
		if (!esc)
		{
			level = atoi (str);
#ifndef SPEAR
			if (level>0 && level<11)
#elif defined(SPEARDEMO)
			if (level>0 && level<2)
#else
			if (level>0 && level<22)
#endif
			{
				gamestate.mapon = level-1;
				playstate = ex_warped;
			}
		}
		return 1;
	}

	DrawPlayBorder();
	
	return 0;
}
Esempio n. 5
0
void
EventQueue::OnSignal(int signo)
{
  Quit();
}
Esempio n. 6
0
void QuitEmulator(void)
{
	Quit();
}
Esempio n. 7
0
void DeplanePic (int picnum)
{
	byte		far *plane0,far *plane1,far *plane2,far *plane3;
	byte		by0,by1,by2,by3;
	unsigned	x,y,b,color,shift,width,height;
	byte		*dest;

//
// convert ega pixels to byte color values in a temp buffer
//
	width = pictable[picnum-STARTPICS].width;
	height = pictable[picnum-STARTPICS].height;

	if (width>8 || height!=64)
		Quit ("DePlanePic: Bad size shape");

	memset (spotvis,BACKGROUNDPIX,sizeof(spotvis));

	plane0 = (byte _seg *)grsegs[picnum];
	plane1 = plane0 + width*height;
	plane2 = plane1 + width*height;
	plane3 = plane2 + width*height;

	for (y=0;y<height;y++)
	{
		dest = &spotvis[y][0];
		for (x=0;x<width;x++)
		{
			by0 = *plane0++;
			by1 = *plane1++;
			by2 = *plane2++;
			by3 = *plane3++;

			for (b=0;b<8;b++)
			{
				shift=8-b;

				color = 0;
				asm	mov	cl,[BYTE PTR shift]
				asm	mov	al,[BYTE PTR by3]
				asm	rcr	al,cl;
				asm	rcl	[BYTE PTR color],1;

				asm	mov	cl,[BYTE PTR shift]
				asm	mov	al,[BYTE PTR by2]
				asm	rcr	al,cl;
				asm	rcl	[BYTE PTR color],1;

				asm	mov	cl,[BYTE PTR shift]
				asm	mov	al,[BYTE PTR by1]
				asm	rcr	al,cl;
				asm	rcl	[BYTE PTR color],1;

				asm	mov	cl,[BYTE PTR shift]
				asm	mov	al,[BYTE PTR by0]
				asm	rcr	al,cl;
				asm	rcl	[BYTE PTR color],1;

				*dest++ = color;
			}	// B
		}		// X
	}			// Y
}
Esempio n. 8
0
LRESULT CALLBACK WndProc(HWND hwnd, UINT message, WPARAM wParam, LPARAM lParam) {
	static UINT X = CLOCK_SIZE, Y = 2 * CLOCK_SIZE, unDir = 1;
	PAINTSTRUCT PtStr;
	HDC hDC;
	POINT stPos;
	static char lwP[20];
	
	switch(message) {
	case WM_TIMER:
		CreateClockPic ();
  		InvalidateRect (hwnd, 0, FALSE);
		//不要使用SendMessage (hwnd, WM_MOVE, 0, 20 * 1024 + 800);
		//使用如下代码
		if (unDir) X += 5;
		else	X-=5;
		if (X <= 0) unDir = 1;
		else if (X >= 1024-CLOCK_SIZE) unDir = 0;
		MoveWindow(hwnd, X, Y, CLOCK_SIZE, CLOCK_SIZE, TRUE);
		//UpdateWindow(hwnd);
		break;

	case WM_PAINT:
		hDC = BeginPaint (hwnd, &PtStr);
		BitBlt(hDC, PtStr.rcPaint.left, PtStr.rcPaint.top,
			PtStr.rcPaint.right - PtStr.rcPaint.left,
			PtStr.rcPaint.bottom - PtStr.rcPaint.top,
			ghDcClock, PtStr.rcPaint.left, PtStr.rcPaint.top, SRCCOPY);
		/*itoa(h2, lwP, 10);
		TextOut (hDC, 50, 20, lwP, strlen(lwP));
		itoa(hwnd, lwP, 10);
		TextOut (hDC, 50, 40, lwP, strlen(lwP));
		*/EndPaint(hwnd, &PtStr);
		break;

	case WM_CREATE:
		//assert(hWinMain != hwnd);
		//printf("%d %d\n", hWinMain, hwnd);
		hWinMain = hwnd;
		Init();
  		break;


	case WM_COMMAND:
		switch(LOWORD(wParam)){
		case IDM_BACK1:
			dwNowBack = IDB_BACK1;
			CheckMenuRadioItem (hMenu, IDM_BACK1, IDM_BACK2, IDM_BACK1, 0);
			break;

		case IDM_BACK2:
			dwNowBack = IDB_BACK2;
			CheckMenuRadioItem (hMenu, IDM_BACK1, IDM_BACK2, IDM_BACK2, 0);
			break;

		case IDM_CIRCLE1:
			dwNowCircle = IDB_CIRCLE1;
			CheckMenuRadioItem (hMenu, IDM_CIRCLE1, IDM_CIRCLE2, IDM_CIRCLE1, 0);
			break;

		case IDM_CIRCLE2:
			dwNowCircle = IDB_CIRCLE2;
			CheckMenuRadioItem (hMenu, IDM_CIRCLE1, IDM_CIRCLE2, IDM_CIRCLE2, 0);
			break;

		case IDM_EXIT:
			Quit();
			return 0;

		default:
			break;
		}
		DeleteBackGround();
		CreateBackGround();
		CreateClockPic();
		InvalidateRect (hwnd, NULL, FALSE);
		break;

	case WM_CLOSE:
		Quit();
		break;

	case WM_RBUTTONDOWN:
		GetCursorPos (&stPos);
		TrackPopupMenu (hMenu, TPM_LEFTALIGN, stPos.x, stPos.y, 0, hwnd, 0);
		break;

	case WM_LBUTTONDOWN:
		SetCursor (hCursorMove);
		UpdateWindow(hwnd);
		ReleaseCapture();
		SendMessage (hwnd, WM_NCLBUTTONDOWN, HTCAPTION, 0);
		SetCursor (hCursorMain);
		break;

	case WM_DESTROY:
		PostQuitMessage(0);
		break;

	default:
		return DefWindowProc(hwnd, message, wParam, lParam);
	}
	return 0;
}
Esempio n. 9
0
SCORE NWDASimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, PWPath &Path)
	{
	assert(uLengthB > 0 && uLengthA > 0);

	const unsigned uPrefixCountA = uLengthA + 1;
	const unsigned uPrefixCountB = uLengthB + 1;

// Allocate DP matrices
	const size_t LM = uPrefixCountA*uPrefixCountB;
	SCORE *DPL_ = new SCORE[LM];
	SCORE *DPM_ = new SCORE[LM];
	SCORE *DPD_ = new SCORE[LM];
	SCORE *DPE_ = new SCORE[LM];
	SCORE *DPI_ = new SCORE[LM];
	SCORE *DPJ_ = new SCORE[LM];

	char *TBM_ = new char[LM];
	char *TBD_ = new char[LM];
	char *TBE_ = new char[LM];
	char *TBI_ = new char[LM];
	char *TBJ_ = new char[LM];

	memset(TBM_, '?', LM);
	memset(TBD_, '?', LM);
	memset(TBE_, '?', LM);
	memset(TBI_, '?', LM);
	memset(TBJ_, '?', LM);

	DPM(0, 0) = 0;
	DPD(0, 0) = MINUS_INFINITY;
	DPE(0, 0) = MINUS_INFINITY;
	DPI(0, 0) = MINUS_INFINITY;
	DPJ(0, 0) = MINUS_INFINITY;

	DPM(1, 0) = MINUS_INFINITY;
	DPD(1, 0) = PA[0].m_scoreGapOpen;
	DPE(1, 0) = PA[0].m_scoreGapOpen2;
	TBD(1, 0) = 'D';
	TBE(1, 0) = 'E';
	DPI(1, 0) = MINUS_INFINITY;
	DPJ(1, 0) = MINUS_INFINITY;

	DPM(0, 1) = MINUS_INFINITY;
	DPD(0, 1) = MINUS_INFINITY;
	DPE(0, 1) = MINUS_INFINITY;
	DPI(0, 1) = PB[0].m_scoreGapOpen;
	DPJ(0, 1) = PB[0].m_scoreGapOpen2;
	TBI(0, 1) = 'I';
	TBJ(0, 1) = 'J';

// Empty prefix of B is special case
	for (unsigned uPrefixLengthA = 2; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
		{
		DPM(uPrefixLengthA, 0) = MINUS_INFINITY;

		DPD(uPrefixLengthA, 0) = DPD(uPrefixLengthA - 1, 0) + g_scoreGapExtend.get();
		DPE(uPrefixLengthA, 0) = DPE(uPrefixLengthA - 1, 0) + g_scoreGapExtend2.get();

		TBD(uPrefixLengthA, 0) = 'D';
		TBE(uPrefixLengthA, 0) = 'E';

		DPI(uPrefixLengthA, 0) = MINUS_INFINITY;
		DPJ(uPrefixLengthA, 0) = MINUS_INFINITY;
		}

// Empty prefix of A is special case
	for (unsigned uPrefixLengthB = 2; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		DPM(0, uPrefixLengthB) = MINUS_INFINITY;

		DPD(0, uPrefixLengthB) = MINUS_INFINITY;
		DPE(0, uPrefixLengthB) = MINUS_INFINITY;

		DPI(0, uPrefixLengthB) = DPI(0, uPrefixLengthB - 1) + g_scoreGapExtend.get();
		DPJ(0, uPrefixLengthB) = DPJ(0, uPrefixLengthB - 1) + g_scoreGapExtend2.get();

		TBI(0, uPrefixLengthB) = 'I';
		TBJ(0, uPrefixLengthB) = 'J';
		}

// Special case to agree with NWFast, no D-I transitions so...
	DPD(uLengthA, 0) = MINUS_INFINITY;
	DPE(uLengthA, 0) = MINUS_INFINITY;
//	DPI(0, uLengthB) = MINUS_INFINITY;
//	DPJ(0, uLengthB) = MINUS_INFINITY;

// ============
// Main DP loop
// ============
	SCORE scoreGapCloseB = MINUS_INFINITY;
	SCORE scoreGapClose2B = MINUS_INFINITY;
	for (unsigned uPrefixLengthB = 1; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
		{
		const ProfPos &PPB = PB[uPrefixLengthB - 1];

		SCORE scoreGapCloseA = MINUS_INFINITY;
		SCORE scoreGapClose2A = MINUS_INFINITY;
		for (unsigned uPrefixLengthA = 1; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
			{
			const ProfPos &PPA = PA[uPrefixLengthA - 1];

			{
		// Match M=LetterA+LetterB
			SCORE scoreLL = ScoreProfPos2(PPA, PPB);
			DPL(uPrefixLengthA, uPrefixLengthB) = scoreLL;

			SCORE scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1);
			SCORE scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseA;
			SCORE scoreEM = DPE(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapClose2A;
			SCORE scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseB;
			SCORE scoreJM = DPJ(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapClose2B;

			SCORE scoreBest;
			if (scoreMM >= scoreDM && scoreMM >= scoreEM && scoreMM >= scoreIM && scoreMM >= scoreJM)
				{
				scoreBest = scoreMM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else if (scoreDM >= scoreMM && scoreDM >= scoreEM && scoreDM >= scoreIM && scoreDM >= scoreJM)
				{
				scoreBest = scoreDM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'D';
				}
			else if (scoreEM >= scoreMM && scoreEM >= scoreDM && scoreEM >= scoreIM && scoreEM >= scoreJM)
				{
				scoreBest = scoreEM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'E';
				}
			else if (scoreIM >= scoreMM && scoreIM >= scoreDM && scoreIM >= scoreEM && scoreIM >= scoreJM)
				{
				scoreBest = scoreIM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'I';
				}
			else
				{
				assert(scoreJM >= scoreMM && scoreJM >= scoreDM && scoreJM >= scoreEM && scoreJM >= scoreIM);
				scoreBest = scoreJM;
				TBM(uPrefixLengthA, uPrefixLengthB) = 'J';
				}
			DPM(uPrefixLengthA, uPrefixLengthB) = scoreBest + scoreLL;
			}

			{
		// Delete D=LetterA+GapB
			SCORE scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) +
			  PA[uPrefixLengthA-1].m_scoreGapOpen;
			SCORE scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB) + g_scoreGapExtend.get();

			SCORE scoreBest;
			if (scoreMD >= scoreDD)
				{
				scoreBest = scoreMD;
				TBD(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else
				{
				assert(scoreDD >= scoreMD);
				scoreBest = scoreDD;
				TBD(uPrefixLengthA, uPrefixLengthB) = 'D';
				}
			DPD(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

			{
		// Delete E=LetterA+GapB
			SCORE scoreME = DPM(uPrefixLengthA-1, uPrefixLengthB) +
			  PA[uPrefixLengthA-1].m_scoreGapOpen2;
			SCORE scoreEE = DPE(uPrefixLengthA-1, uPrefixLengthB) + g_scoreGapExtend2.get();

			SCORE scoreBest;
			if (scoreME >= scoreEE)
				{
				scoreBest = scoreME;
				TBE(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else
				{
				assert(scoreEE >= scoreME);
				scoreBest = scoreEE;
				TBE(uPrefixLengthA, uPrefixLengthB) = 'E';
				}
			DPE(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

		// Insert I=GapA+LetterB
			{
			SCORE scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) +
			  PB[uPrefixLengthB - 1].m_scoreGapOpen;
			SCORE scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1) + g_scoreGapExtend.get();

			SCORE scoreBest;
			if (scoreMI >= scoreII)
				{
				scoreBest = scoreMI;
				TBI(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else 
				{
				assert(scoreII > scoreMI);
				scoreBest = scoreII;
				TBI(uPrefixLengthA, uPrefixLengthB) = 'I';
				}
			DPI(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

		// Insert J=GapA+LetterB
			{
			SCORE scoreMJ = DPM(uPrefixLengthA, uPrefixLengthB-1) +
			  PB[uPrefixLengthB - 1].m_scoreGapOpen2;
			SCORE scoreJJ = DPJ(uPrefixLengthA, uPrefixLengthB-1) + g_scoreGapExtend2.get();

			SCORE scoreBest;
			if (scoreMJ >= scoreJJ)
				{
				scoreBest = scoreMJ;
				TBJ(uPrefixLengthA, uPrefixLengthB) = 'M';
				}
			else 
				{
				assert(scoreJJ > scoreMJ);
				scoreBest = scoreJJ;
				TBJ(uPrefixLengthA, uPrefixLengthB) = 'J';
				}
			DPJ(uPrefixLengthA, uPrefixLengthB) = scoreBest;
			}

			scoreGapCloseA = PPA.m_scoreGapClose;
			scoreGapClose2A = PPA.m_scoreGapClose2;
			}
		scoreGapCloseB = PPB.m_scoreGapClose;
		scoreGapClose2B = PPB.m_scoreGapClose2;
		}

#if TRACE
	Log("\n");
	Log("DA Simple DPL:\n");
	ListDP(DPL_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPM:\n");
	ListDP(DPM_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPD:\n");
	ListDP(DPD_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPE:\n");
	ListDP(DPE_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPI:\n");
	ListDP(DPI_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple DPJ:\n");
	ListDP(DPJ_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBM:\n");
	ListTB(TBM_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBD:\n");
	ListTB(TBD_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBE:\n");
	ListTB(TBE_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBI:\n");
	ListTB(TBI_, PA, PB, uPrefixCountA, uPrefixCountB);
	Log("\n");
	Log("DA Simple TBJ:\n");
	ListTB(TBJ_, PA, PB, uPrefixCountA, uPrefixCountB);
#endif

// Trace-back
// ==========
	Path.Clear();

// Find last edge
	SCORE M = DPM(uLengthA, uLengthB);
	SCORE D = DPD(uLengthA, uLengthB) + PA[uLengthA-1].m_scoreGapClose;
	SCORE E = DPE(uLengthA, uLengthB) + PA[uLengthA-1].m_scoreGapClose2;
	SCORE I = DPI(uLengthA, uLengthB) + PB[uLengthB-1].m_scoreGapClose;
	SCORE J = DPJ(uLengthA, uLengthB) + PB[uLengthB-1].m_scoreGapClose2;
	char cEdgeType = '?';

	SCORE BestScore = M;
	cEdgeType = 'M';
	if (D > BestScore)
		{
		cEdgeType = 'D';
		BestScore = D;
		}
	if (E > BestScore)
		{
		cEdgeType = 'E';
		BestScore = E;
		}
	if (I > BestScore)
		{
		cEdgeType = 'I';
		BestScore = I;
		}
	if (J > BestScore)
		{
		cEdgeType = 'J';
		BestScore = J;
		}

#if	TRACE
	Log("DA Simple: MAB=%.4g DAB=%.4g EAB=%.4g IAB=%.4g JAB=%.4g best=%c\n",
	  M, D, E, I, J, cEdgeType);
#endif

	unsigned PLA = uLengthA;
	unsigned PLB = uLengthB;
	for (;;)
		{
		PWEdge Edge;
		Edge.cType = XlatEdgeType(cEdgeType);
		Edge.uPrefixLengthA = PLA;
		Edge.uPrefixLengthB = PLB;
#if	TRACE
		Log("Prepend %c%d.%d\n", Edge.cType, PLA, PLB);
#endif
		Path.PrependEdge(Edge);

		switch (cEdgeType)
			{
		case 'M':
			assert(PLA > 0);
			assert(PLB > 0);
			cEdgeType = TBM(PLA, PLB);
			--PLA;
			--PLB;
			break;

		case 'D':
			assert(PLA > 0);
			cEdgeType = TBD(PLA, PLB);
			--PLA;
			break;

		case 'E':
			assert(PLA > 0);
			cEdgeType = TBE(PLA, PLB);
			--PLA;
			break;

		case 'I':
			assert(PLB > 0);
			cEdgeType = TBI(PLA, PLB);
			--PLB;
			break;
		
		case 'J':
			assert(PLB > 0);
			cEdgeType = TBJ(PLA, PLB);
			--PLB;
			break;

		default:
			Quit("Invalid edge %c", cEdgeType);
			}
		if (0 == PLA && 0 == PLB)
			break;
		}
	Path.Validate();

//	SCORE Score = TraceBack(PA, uLengthA, PB, uLengthB, DPM_, DPD_, DPI_, Path);

#if	TRACE
	SCORE scorePath = FastScorePath2(PA, uLengthA, PB, uLengthB, Path);
	Path.LogMe();
	Log("Score = %s Path = %s\n", LocalScoreToStr(BestScore), LocalScoreToStr(scorePath));
#endif

	if (g_bKeepSimpleDP.get())
		{
		g_DPM.get() = DPM_;
		g_DPD.get() = DPD_;
		g_DPE.get() = DPE_;
		g_DPI.get() = DPI_;
		g_DPJ.get() = DPJ_;

		g_TBM.get() = TBM_;
		g_TBD.get() = TBD_;
		g_TBE.get() = TBE_;
		g_TBI.get() = TBI_;
		g_TBJ.get() = TBJ_;
		}
	else
		{
		delete[] DPM_;
		delete[] DPD_;
		delete[] DPE_;
		delete[] DPI_;
		delete[] DPJ_;

		delete[] TBM_;
		delete[] TBD_;
		delete[] TBE_;
		delete[] TBI_;
		delete[] TBJ_;
		}

	return BestScore;
	}
Esempio n. 10
0
void MM_GetPtr (memptr *baseptr,id0_unsigned_long_t size)
{
	mmblocktype id0_far *scan,id0_far *lastscan,id0_far *endscan
				,id0_far *purge,id0_far *next;
	id0_int_t			search;
	id0_unsigned_t	needed,startseg;

	needed = (size+15)/16;		// convert size from bytes to paragraphs

	GETNEWBLOCK;				// fill in start and next after a spot is found
	mmnew->length = needed;
	mmnew->useptr = baseptr;
	mmnew->attributes = BASEATTRIBUTES;

	for (search = 0; search<3; search++)
	{
	//
	// first search:	try to allocate right after the rover, then on up
	// second search: 	search from the head pointer up to the rover
	// third search:	compress memory, then scan from start
		if (search == 1 && mmrover == mmhead)
			search++;

		switch (search)
		{
		case 0:
			lastscan = mmrover;
			scan = mmrover->next;
			endscan = NULL;
			break;
		case 1:
			lastscan = mmhead;
			scan = mmhead->next;
			endscan = mmrover;
			break;
		case 2:
			MM_SortMem ();
			lastscan = mmhead;
			scan = mmhead->next;
			endscan = NULL;
			break;
		}

		startseg = lastscan->start + lastscan->length;

		while (scan != endscan)
		{
			if ((refkeen_current_gamever == BE_GAMEVER_KDREAMS2015) || (scan->start - startseg >= needed))
			{
			//
			// got enough space between the end of lastscan and
			// the start of scan, so throw out anything in the middle
			// and allocate the new block
			//
				purge = lastscan->next;
				lastscan->next = mmnew;
				if (refkeen_current_gamever == BE_GAMEVER_KDREAMS2015)
				{
					// Add a few more bytes as a workaround for vanilla bugs
					// in places like CA_HuffExpand
					*baseptr = malloc(size+16);
					if (*baseptr == NULL)
						Quit ("Out of memory!  Please make sure you have enough free memory.");
				}
				else
				{
					mmnew->start /*= *(id0_unsigned_t *)baseptr*/ = startseg;
					*baseptr = EMULATED_SEG_TO_PTR(startseg);
				}
				mmnew->next = scan;
				while ( purge != scan)
				{	// free the purgable block
					next = purge->next;
					FREEBLOCK(purge);
					purge = next;		// purge another if not at scan
				}
				mmrover = mmnew;
				return;	// good allocation!
			}

			//
			// if this block is purge level zero or locked, skip past it
			//
			if ( (scan->attributes & LOCKBIT)
				|| !(scan->attributes & PURGEBITS) )
			{
				lastscan = scan;
				startseg = lastscan->start + lastscan->length;
			}


			scan=scan->next;		// look at next line
		}
	}

	Quit ((current_gamever_int < 110) ? "MM_GetPtr: Out of memory!" : "Out of memory!  Please make sure you have enough free memory.");
}
Esempio n. 11
0
void CIRCSock::ReadLine(const CString& sData) {
	CString sLine = sData;

	sLine.TrimRight("\n\r");

	DEBUG("(" << m_pUser->GetUserName() << ") IRC -> ZNC [" << sLine << "]");

	MODULECALL(OnRaw(sLine), m_pUser, NULL, return);

	if (sLine.Equals("PING ", false, 5)) {
		// Generate a reply and don't forward this to any user,
		// we don't want any PING forwarded
		PutIRC("PONG " + sLine.substr(5));
		return;
	} else if (sLine.Token(1).Equals("PONG")) {
		// Block PONGs, we already responded to the pings
		return;
	} else if (sLine.Equals("ERROR ", false, 6)) {
		//ERROR :Closing Link: nick[24.24.24.24] (Excess Flood)
		CString sError(sLine.substr(6));

		if (sError.Left(1) == ":") {
			sError.LeftChomp();
		}

		m_pUser->PutStatus("Error from Server [" + sError + "]");
		return;
	}

	CString sCmd = sLine.Token(1);

	if ((sCmd.length() == 3) && (isdigit(sCmd[0])) && (isdigit(sCmd[1])) && (isdigit(sCmd[2]))) {
		CString sServer = sLine.Token(0); sServer.LeftChomp();
		unsigned int uRaw = sCmd.ToUInt();
		CString sNick = sLine.Token(2);
		CString sRest = sLine.Token(3, true);

		switch (uRaw) {
			case 1: { // :irc.server.com 001 nick :Welcome to the Internet Relay Network nick
				if (m_bAuthed && sServer == "irc.znc.in") {
					// m_bAuthed == true => we already received another 001 => we might be in a traffic loop
					m_pUser->PutStatus("ZNC seems to be connected to itself, disconnecting...");
					Quit();
					return;
				}

				m_pUser->SetIRCServer(sServer);
				SetTimeout(240, TMO_READ);  // Now that we are connected, let nature take its course
				PutIRC("WHO " + sNick);

				m_bAuthed = true;
				m_pUser->PutStatus("Connected!");

				vector<CClient*>& vClients = m_pUser->GetClients();

				for (unsigned int a = 0; a < vClients.size(); a++) {
					CClient* pClient = vClients[a];
					CString sClientNick = pClient->GetNick(false);

					if (!sClientNick.Equals(sNick)) {
						// If they connected with a nick that doesn't match the one we got on irc, then we need to update them
						pClient->PutClient(":" + sClientNick + "!" + m_Nick.GetIdent() + "@" + m_Nick.GetHost() + " NICK :" + sNick);
					}
				}

				SetNick(sNick);

				MODULECALL(OnIRCConnected(), m_pUser, NULL, );

				m_pUser->ClearRawBuffer();
				m_pUser->AddRawBuffer(":" + sServer + " " + sCmd + " ", " " + sRest);

				CZNC::Get().ReleaseISpoof();
				m_bISpoofReleased = true;

				break;
			}
			case 5:
				ParseISupport(sRest);
				m_pUser->UpdateExactRawBuffer(":" + sServer + " " + sCmd + " ", " " + sRest);
				break;
			case 2:
			case 3:
			case 4:
			case 250:  // highest connection count
			case 251:  // user count
			case 252:  // oper count
			case 254:  // channel count
			case 255:  // client count
			case 265:  // local users
			case 266:  // global users
				m_pUser->UpdateRawBuffer(":" + sServer + " " + sCmd + " ", " " + sRest);
				break;
			case 305:
				m_pUser->SetIRCAway(false);
				break;
			case 306:
				m_pUser->SetIRCAway(true);
				break;
			case 324: {  // MODE
				sRest.Trim();
				CChan* pChan = m_pUser->FindChan(sRest.Token(0));

				if (pChan) {
					pChan->SetModes(sRest.Token(1, true));
				}
			}
				break;
			case 329: {
				sRest.Trim();
				CChan* pChan = m_pUser->FindChan(sRest.Token(0));

				if (pChan) {
					unsigned long ulDate = sLine.Token(4).ToULong();
					pChan->SetCreationDate(ulDate);
				}
			}
				break;
			case 331: {
				// :irc.server.com 331 yournick #chan :No topic is set.
				CChan* pChan = m_pUser->FindChan(sLine.Token(3));

				if (pChan) {
					pChan->SetTopic("");
				}

				break;
			}
			case 332: {
				// :irc.server.com 332 yournick #chan :This is a topic
				CChan* pChan = m_pUser->FindChan(sLine.Token(3));

				if (pChan) {
					CString sTopic = sLine.Token(4, true);
					sTopic.LeftChomp();
					pChan->SetTopic(sTopic);
				}

				break;
			}
			case 333: {
				// :irc.server.com 333 yournick #chan setternick 1112320796
				CChan* pChan = m_pUser->FindChan(sLine.Token(3));

				if (pChan) {
					sNick = sLine.Token(4);
					unsigned long ulDate = sLine.Token(5).ToULong();

					pChan->SetTopicOwner(sNick);
					pChan->SetTopicDate(ulDate);
				}

				break;
			}
			case 352: {
				// :irc.yourserver.com 352 yournick #chan ident theirhost.com irc.theirserver.com theirnick H :0 Real Name
				sServer = sLine.Token(0);
				sNick = sLine.Token(7);
				CString sIdent = sLine.Token(4);
				CString sHost = sLine.Token(5);

				sServer.LeftChomp();

				if (sNick.Equals(GetNick())) {
					m_Nick.SetIdent(sIdent);
					m_Nick.SetHost(sHost);
				}

				m_pUser->SetIRCNick(m_Nick);
				m_pUser->SetIRCServer(sServer);

				const vector<CChan*>& vChans = m_pUser->GetChans();

				for (unsigned int a = 0; a < vChans.size(); a++) {
					vChans[a]->OnWho(sNick, sIdent, sHost);
				}

				break;
			}
			case 353: {  // NAMES
				sRest.Trim();
				// Todo: allow for non @+= server msgs
				CChan* pChan = m_pUser->FindChan(sRest.Token(1));
				// If we don't know that channel, some client might have
				// requested a /names for it and we really should forward this.
				if (pChan) {
					CString sNicks = sRest.Token(2, true);
					if (sNicks.Left(1) == ":") {
						sNicks.LeftChomp();
					}

					pChan->AddNicks(sNicks);
				}

				ForwardRaw353(sLine);

				// We forwarded it already, so return
				return;
			}
			case 366: {  // end of names list
				m_pUser->PutUser(sLine);  // First send them the raw

				// :irc.server.com 366 nick #chan :End of /NAMES list.
				CChan* pChan = m_pUser->FindChan(sRest.Token(0));

				if (pChan) {
					if (pChan->IsOn()) {
						// If we are the only one in the chan, set our default modes
						if (pChan->GetNickCount() == 1) {
							CString sModes = pChan->GetDefaultModes();

							if (sModes.empty()) {
								sModes = m_pUser->GetDefaultChanModes();
							}

							if (!sModes.empty()) {
								PutIRC("MODE " + pChan->GetName() + " " + sModes);
							}
						}
					}
				}

				return;  // return so we don't send them the raw twice
			}
			case 375:  // begin motd
			case 422:  // MOTD File is missing
				m_pUser->ClearMotdBuffer();
			case 372:  // motd
			case 376:  // end motd
				m_pUser->AddMotdBuffer(":" + sServer + " " + sCmd + " ", " " + sRest);
				break;
			case 437:
				// :irc.server.net 437 * badnick :Nick/channel is temporarily unavailable
				// :irc.server.net 437 mynick badnick :Nick/channel is temporarily unavailable
				// :irc.server.net 437 mynick badnick :Cannot change nickname while banned on channel
				if (m_pUser->IsChan(sRest.Token(0)) || sNick != "*")
					break;
			case 432: // :irc.server.com 432 * nick :Erroneous Nickname: Illegal characters
			case 433: {
				CString sBadNick = sRest.Token(0);

				if (!m_bAuthed) {
					SendAltNick(sBadNick);
					return;
				}
				break;
			}
			case 451:
				// :irc.server.com 451 CAP :You have not registered
				// Servers that dont support CAP will give us this error, dont send it to the client
				if (sNick.Equals("CAP"))
					return;
			case 470: {
				// :irc.unreal.net 470 mynick [Link] #chan1 has become full, so you are automatically being transferred to the linked channel #chan2
				// :mccaffrey.freenode.net 470 mynick #electronics ##electronics :Forwarding to another channel

				// freenode style numeric
				CChan* pChan = m_pUser->FindChan(sRest.Token(0));
				if (!pChan) {
					// unreal style numeric
					pChan = m_pUser->FindChan(sRest.Token(1));
				}
				if (pChan) {
					pChan->Disable();
					m_pUser->PutStatus("Channel [" + pChan->GetName() + "] is linked to "
							"another channel and was thus disabled.");
				}
				break;
			}
		}
	} else {
Esempio n. 12
0
void MakeRootMSA(const SeqVect &v, const Tree &GuideTree, ProgNode Nodes[],
  MSA &a)
	{
#if	TRACE
	Log("MakeRootMSA Tree=");
	GuideTree.LogMe();
#endif
	const unsigned uSeqCount = v.GetSeqCount();
	unsigned uColCount = uInsane;
	unsigned uSeqIndex = 0;
	const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
	const unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
	const PWPath &RootPath = Nodes[uRootNodeIndex].m_Path;
	const unsigned uRootColCount = RootPath.GetEdgeCount();
	const unsigned uEstringSize = uRootColCount + 1;
	short *Estring1 = new short[uEstringSize];
	short *Estring2 = new short[uEstringSize];
	SetProgressDesc("Root alignment");

	unsigned uTreeNodeIndex = GetFirstNodeIndex(GuideTree);
	do
		{
		Progress(uSeqIndex, uSeqCount);

		unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
		const Seq &s = *(v[uId]);

		Seq sRootE;
		short *es = MakeRootSeqE(s, GuideTree, uTreeNodeIndex, Nodes, sRootE,
		  Estring1, Estring2);
		Nodes[uTreeNodeIndex].m_EstringL = EstringNewCopy(es);

#if	VALIDATE
		Seq sRoot;
		MakeRootSeq(s, GuideTree, uTreeNodeIndex, Nodes, sRoot);
		if (!sRoot.Eq(sRootE))
			{
			Log("sRoot=");
			sRoot.LogMe();
			Log("sRootE=");
			sRootE.LogMe();
			Quit("Root seqs differ");
			}
#if	TRACE
		Log("MakeRootSeq=\n");
		sRoot.LogMe();
#endif
#endif

		if (uInsane == uColCount)
			{
			uColCount = sRootE.Length();
			a.SetSize(uSeqCount, uColCount);
			}
		else
			{
			assert(uColCount == sRootE.Length());
			}
		a.SetSeqName(uSeqIndex, s.GetName());
		a.SetSeqId(uSeqIndex, uId);
		for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
			a.SetChar(uSeqIndex, uColIndex, sRootE[uColIndex]);
		++uSeqIndex;

		uTreeNodeIndex = GetNextNodeIndex(GuideTree, uTreeNodeIndex);
		}
	while (NULL_NEIGHBOR != uTreeNodeIndex);

	delete[] Estring1;
	delete[] Estring2;

	ProgressStepsDone();
	assert(uSeqIndex == uSeqCount);
	}
Esempio n. 13
0
void CFtpDialog::MessageReceived(BMessage *msg)
{
	switch (msg->what)
	{
		case 'cnct':
			Connect();
			break;

		case msg_ServerNameChanged:
			fServerName->MarkAsInvalid(false);
			break;

		case msg_SelectedDirectory:
		{
			BMenuItem *src;
			FailOSErr(msg->FindPointer("source", (void**)&src));

			strcpy(fPath, "/");
			if (src != fDirectoryField->Menu()->ItemAt(0))
			{
				int i = 1;

				while (true)
				{
					if (i >= fDirectoryField->Menu()->CountItems())
						break;

					BMenuItem *I = fDirectoryField->Menu()->ItemAt(i);

					strcat(fPath, I->Label());
					strcat(fPath, "/");

					if (src == I)
						break;

					++i;
				}
			}

			ChangeDirectory();
			break;
		}

		case msg_SelectedListItem:
		{
			CFtpListItem *i = dynamic_cast<CFtpListItem*>(
				fListView->ItemAt(fListView->CurrentSelection()));
			if (i == reinterpret_cast<CFtpListItem*>(NULL))
			{
				beep();
				return;
			}

			if (i->IsDirectory())
			{
				strcat(fPath, *i);
				strcat(fPath, "/");
				ChangeDirectory();
			}
			else if (OkClicked())
				Quit();
			break;
		}

		case msg_ToggleDot:
			ListDirectory();
			break;

		default:
			HDialog::MessageReceived(msg);
			break;
	}
} // CFtpDialog::MessageReceived
Esempio n. 14
0
  //
  // Recycle
  //
  // Check timer and refund resources once recycled
  //
  void UnitRecycle::StateRecycle()
  {
    // Apply progress
    progressTotal -= progressMax;

    // Has recycling finished
    if (progressTotal <= 0.0F)
    {
      // Refund the resources
      if (subject->GetTeam() && refund > 0)
      {
        // Calculate the total refund
        U32 totalRefund = U32(subject->UnitType()->GetRecyclePercentage() * refund);

        // Add to the team
        subject->GetTeam()->AddResourceStore(totalRefund);

        // Report the resource type
        subject->GetTeam()->ReportResource(totalRefund, "resource.recycled");

        // Generate a message
        if (Team::GetDisplayTeam() == subject->GetTeam())
        {
          CON_MSG((TRANSLATE(("#game.messages.recyclerefund", 2, subject->GetUpgradedUnit().GetDesc(), totalRefund))));
        }
      }

      // Trigger finish FX
      subject->StartGenericFX(0x2062BAAD, NULL, TRUE); // "Recycle::Finish"

      // Did this building consume its constructor
      if 
      (
        subject->UnitType()->GetConstructorType() && 
        !subject->UnitType()->GetConstructorType()->GetIsFacility() &&
        subject->UnitType()->GetConstructorConsume()
      )
      {
        // Ensure the constructors resources are initialized
        subject->UnitType()->GetConstructorType()->InitializeResources();

        // Create a fresh new constructor
        UnitObj *unit = subject->UnitType()->GetConstructorType()->SpawnClosest
        (
          subject->Position(), subject->GetTeam()
        );

        // If this team is controlled by AI then assign the 
        // constructor to the primary base (if there is one)
        if (unit && unit->GetTeam() && unit->GetTeam()->IsAI())
        {
          Strategic::Object *object = unit->GetTeam()->GetStrategicObject();
          if (object)
          {
            Strategic::Base *base = object->GetBaseManager().GetPrimaryBase();

            if (base)
            {
              base->AddUnit(unit);
              base->AddConstructor(unit);
            }
          }
        }
      }

      // Remove the object
      subject->MarkForDeletion();

      // Remove boarded object
      if (subject->UnitType()->CanBoard() && subject->GetBoardManager()->InUse())
      {
        subject->GetBoardManager()->GetUnitObj()->SelfDestruct();
      }

      // Recycle completed
      Quit();
    }
  }
Esempio n. 15
0
void MSA::GetFractionalWeightedCounts(unsigned uColIndex, bool bNormalize,
  FCOUNT fcCounts[], FCOUNT *ptrfcGapStart, FCOUNT *ptrfcGapEnd,
  FCOUNT *ptrfcGapExtend, FCOUNT *ptrfOcc,
  FCOUNT *ptrfcLL, FCOUNT *ptrfcLG, FCOUNT *ptrfcGL, FCOUNT *ptrfcGG) const
	{
	const unsigned uSeqCount = GetSeqCount();
	const unsigned uColCount = GetColCount();
	const char* seqName;
	memset(fcCounts, 0, g_AlphaSize*sizeof(FCOUNT));
	WEIGHT wTotal = 0;
	FCOUNT fGap = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		const WEIGHT w = GetSeqWeight(uSeqIndex);
		if (IsGap(uSeqIndex, uColIndex))
			{
			fGap += w;
			continue;
			}
		else if (IsWildcard(uSeqIndex, uColIndex))
			{
			const unsigned uLetter = GetLetterEx(uSeqIndex, uColIndex);
			switch (g_Alpha)
				{
			case ALPHA_Amino:
				switch (uLetter)
					{
				case AX_B:		// D or N
					fcCounts[AX_D] += w/2;
					fcCounts[AX_N] += w/2;
					break;
				case AX_Z:		// E or Q
					fcCounts[AX_E] += w/2;
					fcCounts[AX_Q] += w/2;
					break;
				default:		// any
					{
					const FCOUNT f = w/20;
					for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
						fcCounts[uLetter] += f;
					break;
					}
					}
				break;

			case ALPHA_DNA:
			case ALPHA_RNA:
				switch (uLetter)
					{
				case AX_R:	// G or A
					fcCounts[NX_G] += w/2;
					fcCounts[NX_A] += w/2;
					break;
				case AX_Y:	// C or T/U
					fcCounts[NX_C] += w/2;
					fcCounts[NX_T] += w/2;
					break;
				default:	// any
					const FCOUNT f = w/20;
					for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
						fcCounts[uLetter] += f;
					break;
					}
				break;

			default:
				Quit("Alphabet %d not supported", g_Alpha);
				}
			continue;
			}
		unsigned uLetter = GetLetter(uSeqIndex, uColIndex);

		//BEGIN MODIFICATIONS TO MUSCLE

		int original=0;
		for(unsigned i=0; i<uColIndex; i++){
			if (i >= this->GetColCount()){break;}
			++original;
			char c = GetChar(uSeqIndex, i);
			if(c== '-'){
				original--;
			}
		}
		seqName = this->GetSeqName(uSeqIndex);
		int compositeVectPosition;
		compositeVectPosition = atoi(seqName);
		CompositeVect CV = *CVLocation;

		Composite* CVL = CV[compositeVectPosition];
		Composite C = *CVL;
		
		for(int j=0; j<21; j++){
			fcCounts[j] = w*C[original][j];
			wTotal = w*C[original][j];
		}

		//ORIGINAL MUSLCE LINE WAS:
		//fcCounts[uLetter] += w;
		//wTotal += w;
		//END MODIFICATIONS TO MUSCLE

		}
	*ptrfOcc = (float) (1.0 - fGap);

	if (bNormalize && wTotal > 0)
		{
		if (wTotal > 1.001)
			Quit("wTotal=%g\n", wTotal);
		for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)
			fcCounts[uLetter] /= wTotal;
//		AssertNormalized(fcCounts);
		}

	FCOUNT fcStartCount = 0;
	if (uColIndex == 0)
		{
		for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
			if (IsGap(uSeqIndex, uColIndex))
				fcStartCount += GetSeqWeight(uSeqIndex);
		}
	else
		{
		for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
			if (IsGap(uSeqIndex, uColIndex) && !IsGap(uSeqIndex, uColIndex - 1))
				fcStartCount += GetSeqWeight(uSeqIndex);
		}

	FCOUNT fcEndCount = 0;
	if (uColCount - 1 == uColIndex)
		{
		for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
			if (IsGap(uSeqIndex, uColIndex))
				fcEndCount += GetSeqWeight(uSeqIndex);
		}
	else
		{
		for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
			if (IsGap(uSeqIndex, uColIndex) && !IsGap(uSeqIndex, uColIndex + 1))
				fcEndCount += GetSeqWeight(uSeqIndex);
		}

	FCOUNT LL = 0;
	FCOUNT LG = 0;
	FCOUNT GL = 0;
	FCOUNT GG = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		WEIGHT w = GetSeqWeight(uSeqIndex);
		bool bLetterHere = !IsGap(uSeqIndex, uColIndex);
		bool bLetterPrev = (uColIndex == 0 || !IsGap(uSeqIndex, uColIndex - 1));
		if (bLetterHere)
			{
			if (bLetterPrev)
				LL += w;
			else
				GL += w;
			}
		else
			{
			if (bLetterPrev)
				LG += w;
			else
				GG += w;
			}
		}

	FCOUNT fcExtendCount = 0;
	if (uColIndex > 0 && uColIndex < GetColCount() - 1)
		for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
			if (IsGap(uSeqIndex, uColIndex) && IsGap(uSeqIndex, uColIndex - 1) &&
			  IsGap(uSeqIndex, uColIndex + 1))
				fcExtendCount += GetSeqWeight(uSeqIndex);

	*ptrfcLL = LL;
	*ptrfcLG = LG;
	*ptrfcGL = GL;
	*ptrfcGG = GG;
	*ptrfcGapStart = fcStartCount;
	*ptrfcGapEnd = fcEndCount;
	*ptrfcGapExtend = fcExtendCount;
	}
Esempio n. 16
0
void
UrlWrapper::ReadyToRun(void)
{
	Quit();
}
Esempio n. 17
0
int main(int argc, char **argv)
{
	char str[256];
	int16 i16;
	HANDLE rom_fh;
	const char *rom_path;
	uint32 rom_size;
	DWORD actual;
	uint8 *rom_tmp;

	// Initialize variables
	RAMBase = 0;

	// Print some info
	printf(GetString(STR_ABOUT_TEXT1), VERSION_MAJOR, VERSION_MINOR);
	printf(" %s\n", GetString(STR_ABOUT_TEXT2));

	// Read preferences
	PrefsInit(NULL, argc, argv);

	// Parse command line arguments
	for (int i=1; i<argc; i++) {
		if (strcmp(argv[i], "--help") == 0) {
			usage(argv[0]);
		} else if (argv[i][0] == '-') {
			fprintf(stderr, "Unrecognized option '%s'\n", argv[i]);
			usage(argv[0]);
		}
	}

	// Check we are using a Windows NT kernel >= 4.0
	OSVERSIONINFO osvi;
	ZeroMemory(&osvi, sizeof(OSVERSIONINFO));
	osvi.dwOSVersionInfoSize = sizeof(OSVERSIONINFO);
	if (!GetVersionEx(&osvi)) {
		ErrorAlert("Could not determine OS type");
		QuitEmulator();
	}
	win_os = osvi.dwPlatformId;
	win_os_major = osvi.dwMajorVersion;
	if (win_os != VER_PLATFORM_WIN32_NT || win_os_major < 4) {
		ErrorAlert(GetString(STR_NO_WIN32_NT_4));
		QuitEmulator();
	}

	// Check that drivers are installed
	if (!check_drivers())
		QuitEmulator();

	// Load win32 libraries
	KernelInit();

	// FIXME: default to DIB driver
	if (getenv("SDL_VIDEODRIVER") == NULL)
	    putenv("SDL_VIDEODRIVER=windib");

	// Initialize SDL system
	int sdl_flags = 0;
#ifdef USE_SDL_VIDEO
	sdl_flags |= SDL_INIT_VIDEO;
#endif
#ifdef USE_SDL_AUDIO
	sdl_flags |= SDL_INIT_AUDIO;
#endif
	assert(sdl_flags != 0);
	if (SDL_Init(sdl_flags) == -1) {
		char str[256];
		sprintf(str, "Could not initialize SDL: %s.\n", SDL_GetError());
		ErrorAlert(str);
		goto quit;
	}
	atexit(SDL_Quit);

#ifdef ENABLE_MON
	// Initialize mon
	mon_init();
#endif

	// Install SIGSEGV handler for CPU emulator
	if (!sigsegv_install_handler(sigsegv_handler)) {
		sprintf(str, GetString(STR_SIGSEGV_INSTALL_ERR), strerror(errno));
		ErrorAlert(str);
		goto quit;
	}

	// Initialize VM system
	vm_init();

	// Get system info
	PVR = 0x00040000;			// Default: 604
	CPUClockSpeed = 100000000;	// Default: 100MHz
	BusClockSpeed = 100000000;	// Default: 100MHz
	TimebaseSpeed =  25000000;	// Default:  25MHz
	PVR = 0x000c0000;			// Default: 7400 (with AltiVec)
	D(bug("PVR: %08x (assumed)\n", PVR));

	// Init system routines
	SysInit();

	// Show preferences editor
	if (!PrefsFindBool("nogui"))
		if (!PrefsEditor())
			goto quit;

	// Create areas for Kernel Data
	if (!kernel_data_init())
		goto quit;
	kernel_data = (KernelData *)Mac2HostAddr(KERNEL_DATA_BASE);
	emulator_data = &kernel_data->ed;
	KernelDataAddr = KERNEL_DATA_BASE;
	D(bug("Kernel Data at %p (%08x)\n", kernel_data, KERNEL_DATA_BASE));
	D(bug("Emulator Data at %p (%08x)\n", emulator_data, KERNEL_DATA_BASE + offsetof(KernelData, ed)));

	// Create area for DR Cache
	if (vm_mac_acquire(DR_EMULATOR_BASE, DR_EMULATOR_SIZE) < 0) {
		sprintf(str, GetString(STR_DR_EMULATOR_MMAP_ERR), strerror(errno));
		ErrorAlert(str);
		goto quit;
	}
	dr_emulator_area_mapped = true;
	if (vm_mac_acquire(DR_CACHE_BASE, DR_CACHE_SIZE) < 0) {
		sprintf(str, GetString(STR_DR_CACHE_MMAP_ERR), strerror(errno));
		ErrorAlert(str);
		goto quit;
	}
	dr_cache_area_mapped = true;
	DRCacheAddr = (uint32)Mac2HostAddr(DR_CACHE_BASE);
	D(bug("DR Cache at %p (%08x)\n", DRCacheAddr, DR_CACHE_BASE));

	// Create area for SheepShaver data
	if (!SheepMem::Init()) {
		sprintf(str, GetString(STR_SHEEP_MEM_MMAP_ERR), strerror(errno));
		ErrorAlert(str);
		goto quit;
	}

	// Create area for Mac ROM
	if (vm_mac_acquire(ROM_BASE, ROM_AREA_SIZE) < 0) {
		sprintf(str, GetString(STR_ROM_MMAP_ERR), strerror(errno));
		ErrorAlert(str);
		goto quit;
	}
	ROMBase = ROM_BASE;
	ROMBaseHost = Mac2HostAddr(ROMBase);
	rom_area_mapped = true;
	D(bug("ROM area at %p (%08x)\n", ROMBaseHost, ROMBase));

	// Create area for Mac RAM
	RAMSize = PrefsFindInt32("ramsize");
	if (RAMSize < 8*1024*1024) {
		WarningAlert(GetString(STR_SMALL_RAM_WARN));
		RAMSize = 8*1024*1024;
	}
	RAMBase = 0;
	if (vm_mac_acquire(RAMBase, RAMSize) < 0) {
		sprintf(str, GetString(STR_RAM_MMAP_ERR), strerror(errno));
		ErrorAlert(str);
		goto quit;
	}
	RAMBaseHost = Mac2HostAddr(RAMBase);
	ram_area_mapped = true;
	D(bug("RAM area at %p (%08x)\n", RAMBaseHost, RAMBase));

	if (RAMBase > ROMBase) {
		ErrorAlert(GetString(STR_RAM_HIGHER_THAN_ROM_ERR));
		goto quit;
	}

	// Load Mac ROM
	rom_path = PrefsFindString("rom");
	rom_fh = CreateFile(rom_path && *rom_path ? rom_path : ROM_FILE_NAME,
						GENERIC_READ, 0, NULL, OPEN_EXISTING,
						FILE_ATTRIBUTE_NORMAL, NULL);

	if (rom_fh == INVALID_HANDLE_VALUE) {
		rom_fh = CreateFile(ROM_FILE_NAME2,
							GENERIC_READ, 0, NULL, OPEN_EXISTING,
							FILE_ATTRIBUTE_NORMAL, NULL);

		if (rom_fh == INVALID_HANDLE_VALUE) {
			ErrorAlert(GetString(STR_NO_ROM_FILE_ERR));
			goto quit;
		}
	}
	printf(GetString(STR_READING_ROM_FILE));
	rom_size = GetFileSize(rom_fh, NULL);
	rom_tmp = new uint8[ROM_SIZE];
	ReadFile(rom_fh, (void *)rom_tmp, ROM_SIZE, &actual, NULL);
	CloseHandle(rom_fh);
	
	// Decode Mac ROM
	if (!DecodeROM(rom_tmp, actual)) {
		if (rom_size != 4*1024*1024) {
			ErrorAlert(GetString(STR_ROM_SIZE_ERR));
			goto quit;
		} else {
			ErrorAlert(GetString(STR_ROM_FILE_READ_ERR));
			goto quit;
		}
	}
	delete[] rom_tmp;
	
	// Initialize native timers
	timer_init();

	// Initialize everything
	if (!InitAll(NULL))
		goto quit;
	D(bug("Initialization complete\n"));

	// Write protect ROM
	vm_protect(ROMBaseHost, ROM_AREA_SIZE, VM_PAGE_READ);

	// Start 60Hz thread
	tick_thread_cancel = false;
	tick_thread_active = ((tick_thread = create_thread(tick_func)) != NULL);
	SetThreadPriority(tick_thread, THREAD_PRIORITY_ABOVE_NORMAL);
	D(bug("Tick thread installed (%ld)\n", tick_thread));

	// Start NVRAM watchdog thread
	memcpy(last_xpram, XPRAM, XPRAM_SIZE);
	nvram_thread_cancel = false;
	nvram_thread_active = ((nvram_thread = create_thread(nvram_func, NULL)) != NULL);
	SetThreadPriority(nvram_thread, THREAD_PRIORITY_BELOW_NORMAL);
	D(bug("NVRAM thread installed (%ld)\n", nvram_thread));

	// Get my thread ID and jump to ROM boot routine
	emul_thread = GetCurrentThread();
	D(bug("Jumping to ROM\n"));
#ifdef _MSC_VER
	__try {
#endif
		jump_to_rom(ROMBase + 0x310000);
#ifdef _MSC_VER
	} __except (main_exception_filter(GetExceptionInformation())) {}
#endif
	D(bug("Returned from ROM\n"));

quit:
	Quit();
	return 0;
}
void PM_Startup()
{
    char fname[13] = "vswap.";
    strcat(fname,extension);

    FILE *file = fopen(fname,"rb");
    if(!file)
        CA_CannotOpen(fname);

    ChunksInFile = 0;
    fread(&ChunksInFile, sizeof(word), 1, file);
    PMSpriteStart = 0;
    fread(&PMSpriteStart, sizeof(word), 1, file);
    PMSoundStart = 0;
    fread(&PMSoundStart, sizeof(word), 1, file);

    uint32_t* pageOffsets = (uint32_t *) malloc((ChunksInFile + 1) * sizeof(int32_t));
    CHECKMALLOCRESULT(pageOffsets);
    fread(pageOffsets, sizeof(uint32_t), ChunksInFile, file);

    word *pageLengths = (word *) malloc(ChunksInFile * sizeof(word));
    CHECKMALLOCRESULT(pageLengths);
    fread(pageLengths, sizeof(word), ChunksInFile, file);

    fseek(file, 0, SEEK_END);
    long fileSize = ftell(file);
    long pageDataSize = fileSize - pageOffsets[0];
    if(pageDataSize > (size_t) -1)
        Quit("The page file \"%s\" is too large!", fname);

    pageOffsets[ChunksInFile] = fileSize;

    uint32_t dataStart = pageOffsets[0];
    int i;

    // Check that all pageOffsets are valid
    for(i = 0; i < ChunksInFile; i++)
    {
        if(!pageOffsets[i]) continue;   // sparse page
        if(pageOffsets[i] < dataStart || pageOffsets[i] >= (size_t) fileSize)
            Quit("Illegal page offset for page %i: %u (filesize: %u)",
                    i, pageOffsets[i], fileSize);
    }

    // Calculate total amount of padding needed for sprites and sound info page
    int alignPadding = 0;
    for(i = PMSpriteStart; i < PMSoundStart; i++)
    {
        if(!pageOffsets[i]) continue;   // sparse page
        uint32_t offs = pageOffsets[i] - dataStart + alignPadding;
        if(offs & 1)
            alignPadding++;
    }

    if((pageOffsets[ChunksInFile - 1] - dataStart + alignPadding) & 1)
        alignPadding++;

    PMPageDataSize = (size_t) pageDataSize + alignPadding;
    PMPageData = (uint32_t *) malloc(PMPageDataSize);
    CHECKMALLOCRESULT(PMPageData);

    PMPages = (uint8_t **) malloc((ChunksInFile + 1) * sizeof(uint8_t *));
    CHECKMALLOCRESULT(PMPages);

    // Load pages and initialize PMPages pointers
    uint8_t *ptr = (uint8_t *) PMPageData;
    for(i = 0; i < ChunksInFile; i++)
    {
        if(i >= PMSpriteStart && i < PMSoundStart || i == ChunksInFile - 1)
        {
            size_t offs = ptr - (uint8_t *) PMPageData;

            // pad with zeros to make it 2-byte aligned
            if(offs & 1)
            {
                *ptr++ = 0;
                if(i == ChunksInFile - 1) PMSoundInfoPagePadded = true;
            }
        }

        PMPages[i] = ptr;

        if(!pageOffsets[i])
            continue;               // sparse page

        // Use specified page length, when next page is sparse page.
        // Otherwise, calculate size from the offset difference between this and the next page.
        uint32_t size;
        if(!pageOffsets[i + 1]) size = pageLengths[i];
        else size = pageOffsets[i + 1] - pageOffsets[i];

        fseek(file, pageOffsets[i], SEEK_SET);
        fread(ptr, 1, size, file);
        ptr += size;
    }

    // last page points after page buffer
    PMPages[ChunksInFile] = ptr;

    free(pageLengths);
    free(pageOffsets);
    fclose(file);
}
Esempio n. 19
0
unsigned BuildCompShape (t_compshape _seg **finalspot)
{
	t_compshape 	_seg *work;
	byte		far *code;
	int			firstline,lastline,x,y;
	unsigned	firstpix,lastpix,width;
	unsigned	totalsize,pixelofs;
	unsigned	buff;


//	MM_GetPtr (&(memptr)work,20000);
	EGAWRITEMODE(0);
	EGAREADMAP(0);		// use ega screen memory for temp buffer
	EGAMAPMASK(1);
	buff = screenloc[1];
	work = (t_compshape _seg *)(0xa000+(buff+15)/16);

//
// find the width of the shape
//
	firstline = -1;
	x=0;
	do
	{
		for (y=0;y<64;y++)
			if (spotvis[y][x] != BACKGROUNDPIX)
			{
				firstline = x;
				break;
			}
		if (++x == 64)
			Quit ("BuildCompShape: No shape data!");
	} while (firstline == -1);

	lastline = -1;
	x=63;
	do
	{
		for (y=0;y<64;y++)
			if (spotvis[y][x] != BACKGROUNDPIX)
			{
				lastline = x;
				break;
			}
		x--;
	} while (lastline == -1);

	width = lastline-firstline+1;

	work->width = width;
	code = (byte far *)&work->codeofs[width];

//
// copy all non background pixels to the work space
//
	pixelofs = FP_OFF(code);

	for (x=firstline;x<=lastline;x++)
		for (y=0;y<64;y++)
			if (spotvis[y][x] != BACKGROUNDPIX)
				*code++ = spotvis[y][x];

//
// start compiling the vertical lines
//
	for (x=firstline;x<=lastline;x++)
	{
		work->codeofs[x-firstline] = FP_OFF(code);

		y=0;
		do
		{
		//
		// scan past black background pixels
		//
			while (spotvis[y][x] == BACKGROUNDPIX && y<64)
				y++;

			if (y>63)		// no more segments
				break;

			firstpix = y+1;		// +1 because width is before codeofs

		//
		// scan past scalable pixels
		//
			while (spotvis[y][x] != BACKGROUNDPIX && y<64)
				y++;

			if (y>63)
				lastpix = 65;
			else
				lastpix = y+1;	// actually one pixel past the last displayed

		//
		// compile the scale call
		//
			*code++ = 0x8b;		// mov bx,[lastpix*2]
			*code++ = 0x1e;
			*((unsigned far *)code)++ = lastpix*2;

			*code++ = 0x8b;		// mov cx,[bx]
			*code++ = 0x0f;

			*code++ = 0xc6;		// move [BYTE bx],0xcb
			*code++ = 0x07;
			*code++ = 0xcb;

			*code++ = 0xa1;		// mov ax,[firstpix*2]	/*************
			*((unsigned far *)code)++ = firstpix*2;

			*code++ = 0x36;		// mov [ss:0],ax
			*code++ = 0xa3;
			*code++ = 0x00;
			*code++ = 0x00;

			*code++ = 0x8e;		// mov ds,dx	(mov ds,cs)
			*code++ = 0xda;

			*code++ = 0xbe;		// mov si,OFFSET pixelofs-firstpixel
			*((unsigned far *)code)++ = pixelofs-firstpix;

			*code++ = 0xff;		// call [DWORD bp]
			*code++ = 0x5e;
			*code++ = 0x00;

			*code++ = 0x8e;		// mov ds,[bp+2]
			*code++ = 0x5e;
			*code++ = 0x02;

			*code++ = 0x89;		// mov [bx],cx
			*code++ = 0x0f;

			pixelofs += (lastpix-firstpix);
		} while (y<63);

	//
	// retf
	//
		*code++ = 0xcb;
	}


//
// copy the final shape to a properly sized buffer
//
	totalsize = FP_OFF(code);

	if (totalsize >= (PAGELEN*2))
		Quit("BuildCompShape(): Shape is too complex!");

	MM_GetPtr ((memptr *)finalspot,totalsize);
	_fmemcpy ((byte _seg *)(*finalspot),(byte _seg *)work,totalsize);
//	MM_FreePtr (&(memptr)work);

	return totalsize;
}
Esempio n. 20
0
File: BAM.CPP Progetto: mhjlam1/bam
bool
BAM_Application::HandleMsg(Message* pMsg)
{
 	BAM_TeleportPopup *pTeleport;


	switch(pMsg->type)
	{
		case MSG_NOTICE:
			switch(pMsg->notice.type)
			{
				case N_QUIT:
					return(TRUE);
			}
			break;

		case MSG_EVENT:
			switch (pMsg->event.type)
			{
				case E_KEY_DOWN:
					switch(pMsg->event.value)
					{
						case K_X:
							#ifndef NDEBUG
							if(pMsg->event.modifiers & MOD_ALT)
								pContextMgr->Quit();
							#endif
							break;

						case K_ESC:
							Quit();
							return(TRUE);

						#ifndef NDEBUG
						case K_Z:
							//saveNum = 1;
							if(pMono->suspended)
								pMono->Resume();
							else pMono->Suspend();
							break;

						case K_Y:
							//restoreNum = 1;
							break;

						case K_F4:
							//one screen capture

							if(!bGlobal.gSnap)
							{
								if(!pWorld || (pWorld && bGlobal.storyLine != NETGAME))
								{
									//lets setup for screen snapping (capture)
									TRACK_MEM("Snap");	pSnap = new Snap;
									bGlobal.gSnap = pSnap->gSelf;
								}
							}

							//no single shots while snap is toggled on
							if(!pSnap->snapOn)
								pSnap->SingleScreen();

							//delete snap alloc -now elsewhere
							//if(bGlobal.gSnap)
							//{
							//	ADelete(bGlobal.gSnap);
							//	bGlobal.gSnap = 0;
							//}

							return(TRUE);

						//case K_F6:
							////toggle on/off screen snap
							//
							//if(!bGlobal.gSnap)
							//{
							//	//lets setup for screen snapping (capture)
							//	TRACK_MEM("Snap");	pSnap = new Snap;
							//	bGlobal.gSnap = pSnap->gSelf;
							//}
							//
							//if(pSnap->snapOn)
							//	pSnap->StopSnap();
							//else
							//	pSnap->StartSnap();
						//	return(TRUE);

						case K_F10:
							SetFontColors(CI_SKIP,93,90);
							// teleport
							TRACK_MEM("teleport"); pTeleport = new BAM_TeleportPopup;
							pTeleport->Setup(OPTION_SQB,38);
							return(TRUE);

						case K_F11:
							SetFontColors(CI_SKIP,93,90);
							// RUN CINEMATIC NUMBER?
							//can only use this from main menu
							if(bGlobal.roomMgr.curRoomNum == BR_MENU)
							{
								bGlobal.roomMgr.prevRoomMode = 0;
								bGlobal.roomMgr.newRoomMode = 1;
								TRACK_MEM("telecine"); pTeleport = new BAM_TeleportPopup;
								pTeleport->Setup(OPTION_SQB,53);
							}
							return(TRUE);

						case	K_PRINT_SCREEN:
//							if (!ki_debugging)
//							{
//								#pragma aux ENTER_DEBUG =		\
//									"int	3";
//								ENTER_DEBUG();
//							}
							return(TRUE);
							#endif
					}
			}
	}
	return(Context::HandleMsg(pMsg));
}
Esempio n. 21
0
void ScaleShape (int xcenter, t_compshape _seg *compshape, unsigned scale)
{
	#define MAX_OBJ_SCALE (MAXSCALE)


	t_compscale _seg *comptable;
	unsigned	width,scalewidth;
	int			x,pixel,lastpixel,pixwidth,min;
	unsigned	far *codehandle, far *widthptr;
	unsigned	badcodeptr;
	int			rightclip;

	if (!compshape)
		Quit ("ScaleShape: NULL compshape ptr!");

	scale = (scale+1)/2;
	if (!scale)
		return;								// too far away

	if (scale>MAX_OBJ_SCALE)
		scale = MAX_OBJ_SCALE;

	comptable = scaledirectory[scale];

	width = compshape->width;
	scalewidth = comptable->start[width];

	pixel = xcenter - scalewidth/2;
	lastpixel = pixel+scalewidth-1;

	if (pixel >= VIEWWIDTH || lastpixel < 0)
		return;								// totally off screen

//
// scan backwards from the right edge until pixels are visable
// rightclip is the first NON VISABLE pixel
//
	if (lastpixel>=VIEWWIDTH-1)
		rightclip = VIEWWIDTH-1;
	else
		rightclip = lastpixel;

	if (zbuffer[rightclip]>scale)
	{
		if (pixel>0)
			min = pixel;
		else
			min = 0;
		do
		{
			if (--rightclip < min)
				return;							// totally covered or before 0
			if (zbuffer[rightclip]<=scale)
				break;
		} while (1);
	}
	rightclip++;

//
// scan from the left until it is on screen, leaving
// [pixel],[pixwidth],[codehandle],and [widthptr] set correctly
//
	*(((unsigned *)&longtemp)+1) = (unsigned)compshape;	// seg of shape
	codehandle = &compshape->codeofs[0];
	badcodeptr = compshape->codeofs[width];
	widthptr = &comptable->width[0];
	asm	mov	ax,[comptable]
	asm	mov	WORD PTR [2],ax				// ds:0-4 is used as a far call pointer
										// by the compiled shapes
	pixwidth = *widthptr;				// scaled width of this pixel
	while (!pixwidth)
	{
		pixwidth = *++widthptr;			// find the first visable pixel
		codehandle++;
	}

	if (pixel<0)
	{
		do
		{
			if (pixel+pixwidth>0)
			{
				pixwidth += pixel;
				pixel = 0;
				break;
			}
			do
			{
				pixwidth = *++widthptr;
				codehandle++;
			} while (!pixwidth);
			pixel+=pixwidth;
		} while (1);
	}

//
// scan until it is visable, leaving
// [pixel],[pixwidth],[codehandle],and [widthptr] set correctly
//
	do
	{
		if (zbuffer[pixel] <= scale)
			break;							// start drawing here
		pixel++;
		if (!--pixwidth)
		{
			do
			{
				pixwidth = *++widthptr;
				codehandle++;
			} while (!pixwidth);
		}
	} while (1);

	if (pixel+pixwidth>rightclip)
		pixwidth = rightclip-pixel;
//
// draw lines
//
	do		// while (1)
	{
	//
	// scale a vertical segment [pixwidth] pixels wide at [pixel]
	//
		(unsigned)longtemp = *codehandle;	// offset of compiled code
		if ((unsigned)longtemp == badcodeptr)
			Quit ("ScaleShape: codehandle past end!");

		asm	mov	bx,[pixel]
		asm	mov	di,bx
		asm	shr	di,1
		asm	shr	di,1
		asm	shr	di,1						// X in bytes
		asm	add	di,[bufferofs]
		asm	and	bx,7
		asm	shl	bx,1
		asm	shl	bx,1
		asm	shl	bx,1
		asm	add	bx,[pixwidth]				// bx = pixel*8+pixwidth-1
		asm	dec	bx
		asm	push	bx
		asm	mov	al,BYTE PTR [bitmasks1+bx]
		asm	mov	dx,GC_INDEX+1
		asm	out	dx,al						// set bit mask register

		asm	mov	es,[screenseg]
		asm	push	si
		asm	push	di
		asm	push	bp
		asm	xor	bp,bp
		asm	mov	dx,[WORD PTR longtemp+2]
		asm	mov	ds,[2]
		asm	call ss:[DWORD PTR longtemp]		// scale the line of pixels
		asm	mov	ax,ss
		asm	mov	ds,ax
		asm	pop		bp
		asm	pop		di
		asm	pop		si

		asm	pop	bx
		asm	mov	al,BYTE PTR [bitmasks2+bx]
		asm	or	al,al
		asm	jz	nosecond

	//
	// draw a second byte for vertical strips that cross two bytes
	//
		asm	inc	di
		asm	mov	dx,GC_INDEX+1
		asm	out	dx,al						// set bit mask register
		asm	push	si
		asm	push	di
		asm	push	bp
		asm	xor	bp,bp
		asm	mov	dx,[WORD PTR longtemp+2]
		asm	mov	ds,[2]
		asm	call ss:[DWORD PTR longtemp]		// scale the line of pixels
		asm	mov	ax,ss
		asm	mov	ds,ax
		asm	pop		bp
		asm	pop		di
		asm	pop		si


	//
	// advance to the next drawn line
	//
nosecond:;
		if ( (pixel+=pixwidth) == rightclip )
		{
			asm	mov	WORD PTR [0],0
			asm	mov	WORD PTR [2],0
			return;							// all done!
		}

		do
		{
			pixwidth = *++widthptr;
			codehandle++;
		} while (!pixwidth);

		if (pixel+pixwidth > rightclip)
			pixwidth = rightclip-pixel;

	} while (1);

}
Esempio n. 22
0
void Application::OnInit()
{
  nuiInit(NULL);

  uint Width = 0, Height = 0;
  bool HasSize = false;
  bool IsFullScreen = false;
  bool DebugObject = false;
  bool DebugInfo = false;
  bool ShowFPS = false;

  
  nuiRenderer Renderer = eOpenGL;
//  nuiRenderer Renderer = eSoftware;
//  nuiRenderer Renderer = eDirect3D;

  // Accept NGL default options
  ParseDefaultArgs();

  GetLog().UseConsole(true);
  GetLog().SetLevel(_T("font"), 100);

  // Manual
  if ( (GetArgCount() == 1) &&
       ((!GetArg(0).Compare(_T("-h"))) || (!GetArg(0).Compare(_T("--help")))) )
  {
    NGL_OUT(_T("no params\n"));
    Quit (0);
    return;
  }
  
  // Parse args
  int i = 0;
  while (i < GetArgCount())
  {
    nglString arg = GetArg(i);
    if ((!arg.Compare(_T("--size")) || !arg.Compare(_T("-s"))) && ((i+1) < GetArgCount()))
    {
      int w, h;

      std::string str(GetArg(i+1).GetStdString());
      sscanf(str.c_str(), "%dx%d", &w, &h);
      if (w > 0) Width  = w;
      if (h > 0) Height = h;
      HasSize = true;
      i++;
    }
    else if (!arg.Compare(_T("--showfps")) || !arg.Compare(_T("-fps"))) ShowFPS = true;
    else if (!arg.Compare(_T("--fullscreen")) || !arg.Compare(_T("-f"))) IsFullScreen = true;
    else if (!arg.Compare(_T("--debugobject")) || !arg.Compare(_T("-d"))) DebugObject = true;
    else if (!arg.Compare(_T("--debuginfo")) || !arg.Compare(_T("-i"))) DebugInfo = true;
    else if (!arg.Compare(_T("--renderer")) || !arg.Compare(_T("-r"))) 
    {
      arg = GetArg(i+1);
      if (!arg.Compare(_T("opengl"))) Renderer = eOpenGL;
      else if (!arg.Compare(_T("direct3d"))) Renderer = eDirect3D;
      else if (!arg.Compare(_T("software"))) Renderer = eSoftware;
      i++;
    }
    i++;
  }
  
  nuiMainWindow::SetRenderer(Renderer);

  if (!HasSize)
  {
    if (IsFullScreen)
    {
      nglVideoMode current_mode;

      Width = current_mode.GetWidth();
      Height = current_mode.GetHeight();
    }
    else
    {
#ifdef NUI_IPHONE
      Width = 320;
      Height = 480;
#else
      Width = 800;
      Height = 600;
#endif
    }
  }


  /* Create the nglWindow (and thus a GL context, don't even try to
   *   instantiate the gui (or nglFont) before the nuiWin !)
   */
  nuiContextInfo ContextInfo(nuiContextInfo::StandardContext3D);
  nglWindowInfo Info;

  Info.Flags = IsFullScreen ? nglWindow::FullScreen : 0;
  Info.Width = Width;
  Info.Height = Height;
  Info.Pos = nglWindowInfo::ePosCenter;
  Info.Title = APPLICATION_TITLE;
  Info.XPos = 0;
  Info.YPos = 0;
        
  mpMainWindow = new MainWindow(ContextInfo,Info, ShowFPS);
  if ((!mpMainWindow) || (mpMainWindow->GetError()))
  {
    if (mpMainWindow) 
      NGL_OUT(_T("Error: cannot create window (%s)\n"), mpMainWindow->GetErrorStr());
    Quit (1);
    return;
  }
  mpMainWindow->Acquire();
  mpMainWindow->DBG_SetMouseOverInfo(DebugInfo);  mpMainWindow->DBG_SetMouseOverObject(DebugObject);
  mpMainWindow->SetState(nglWindow::eShow);

}
Esempio n. 23
0
void
MediaAddonServer::ReadyToRun()
{
	if (!be_roster->IsRunning("application/x-vnd.Be.media-server")) {
		// the media server is not running, let's quit
		fprintf(stderr, "The media_server is not running!\n");
		Quit();
		return;
	}

	// the control thread is already running at this point,
	// so we can talk to the media server and also receive
	// commands for instantiation

	ASSERT(fStartup == true);

	// The very first thing to do is to create the system time source,
	// register it with the server, and make it the default SYSTEM_TIME_SOURCE
	BMediaNode *timeSource = new SystemTimeSource;
	status_t result = fMediaRoster->RegisterNode(timeSource);
	if (result != B_OK) {
		fprintf(stderr, "Can't register system time source : %s\n",
			strerror(result));
		debugger("Can't register system time source");
	}

	if (timeSource->ID() != NODE_SYSTEM_TIMESOURCE_ID)
		debugger("System time source got wrong node ID");
	media_node node = timeSource->Node();
	result = MediaRosterEx(fMediaRoster)->SetNode(SYSTEM_TIME_SOURCE, &node);
	if (result != B_OK)
		debugger("Can't setup system time source as default");

	// During startup, first all add-ons are loaded, then all
	// nodes (flavors) representing physical inputs and outputs
	// are instantiated. Next, all add-ons that need autostart
	// will be autostarted. Finally, add-ons that don't have
	// any active nodes (flavors) will be unloaded.

	char parameter[32];
	size_t parameterLength = sizeof(parameter);
	bool safeMode = false;
	if (_kern_get_safemode_option(B_SAFEMODE_SAFE_MODE, parameter,
			&parameterLength) == B_OK) {
		if (!strcasecmp(parameter, "enabled") || !strcasecmp(parameter, "on")
			|| !strcasecmp(parameter, "true") || !strcasecmp(parameter, "yes")
			|| !strcasecmp(parameter, "enable") || !strcmp(parameter, "1"))
			safeMode = true;
	}

	fMonitorHandler = new MonitorHandler(this);
	AddHandler(fMonitorHandler);

	BMessage pulse(B_PULSE);
	fPulseRunner = new BMessageRunner(fMonitorHandler, &pulse, 1000000LL);
		// the monitor handler needs a pulse to check if add-ons are ready

	// load dormant media nodes
	const directory_which directories[] = {
		B_USER_ADDONS_DIRECTORY,
		B_COMMON_ADDONS_DIRECTORY,
		B_SYSTEM_ADDONS_DIRECTORY
	};

	// when safemode, only B_SYSTEM_ADDONS_DIRECTORY is used
	for (uint32 i = safeMode ? 2 : 0;
			i < sizeof(directories) / sizeof(directory_which); i++) {
		BDirectory directory;
		node_ref nodeRef;
		BPath path;
		if (find_directory(directories[i], &path) == B_OK
			&& path.Append("media") == B_OK
			&& directory.SetTo(path.Path()) == B_OK
			&& directory.GetNodeRef(&nodeRef) == B_OK)
			fMonitorHandler->AddDirectory(&nodeRef);
	}

#ifdef USER_ADDON_PATH
	node_ref nodeRef;
	if (entry.SetTo(USER_ADDON_PATH) == B_OK
		&& entry.GetNodeRef(&nodeRef) == B_OK)
		fMonitorHandler->AddDirectory(&nodeRef);
#endif

	fStartup = false;

	InfoMap::iterator iterator = fInfoMap.begin();
	for (; iterator != fInfoMap.end(); iterator++)
		_InstantiatePhysicalInputsAndOutputs(iterator->second);

	for (iterator = fInfoMap.begin(); iterator != fInfoMap.end(); iterator++)
		_InstantiateAutostartFlavors(iterator->second);

	for (iterator = fInfoMap.begin(); iterator != fInfoMap.end(); iterator++)
		_PutAddonIfPossible(iterator->second);

	server_rescan_defaults_command cmd;
	SendToServer(SERVER_RESCAN_DEFAULTS, &cmd, sizeof(cmd));
}
int main(int argc, char** argv)
{
	char glutGamemode[32];
	const char *cparam_name = "Data/camera_para.dat";
	//
	// Camera configuration.
	//
#ifdef _WIN32
	char			*vconf = "Data\\WDM_camera_flipV.xml";
#else
	char			*vconf = "";
#endif
	const char *patt_name  = "Data/patt.hiro";
	
	// ----------------------------------------------------------------------------
	// Library inits.
	//

	glutInit(&argc, argv);

	// ----------------------------------------------------------------------------
	// Hardware setup.
	//

	if (!setupCamera(cparam_name, vconf, &gARTCparam)) {
		fprintf(stderr, "main(): Unable to set up AR camera.\n");
		exit(-1);
	}

	// ----------------------------------------------------------------------------
	// Library setup.
	//

	// Set up GL context(s) for OpenGL to draw into.
	glutInitDisplayMode(GLUT_DOUBLE | GLUT_RGBA | GLUT_DEPTH);
	if (!prefWindowed) {
		if (prefRefresh) sprintf(glutGamemode, "%ix%i:%[email protected]%i", prefWidth, prefHeight, prefDepth, prefRefresh);
		else sprintf(glutGamemode, "%ix%i:%i", prefWidth, prefHeight, prefDepth);
		glutGameModeString(glutGamemode);
		glutEnterGameMode();
	} else {
		glutInitWindowSize(prefWidth, prefHeight);
		glutCreateWindow(argv[0]);
	}

	// Setup argl library for current context.
	if ((gArglSettings = arglSetupForCurrentContext()) == NULL) {
		fprintf(stderr, "main(): arglSetupForCurrentContext() returned error.\n");
		exit(-1);
	}
	debugReportMode(gArglSettings);
	glEnable(GL_DEPTH_TEST);
	arUtilTimerReset();
		
	if (!setupMarker(patt_name, &gPatt_id)) {
		fprintf(stderr, "main(): Unable to set up AR marker.\n");
		Quit();
	}
	
	// Register GLUT event-handling callbacks.
	// NB: Idle() is registered by Visibility.
	glutDisplayFunc(Display);
	glutReshapeFunc(Reshape);
	glutVisibilityFunc(Visibility);
	glutKeyboardFunc(Keyboard);
	
	glutMainLoop();

	return (0);
}
Esempio n. 25
0
void FindDiags(const ProfPos *PX, unsigned uLengthX, const ProfPos *PY,
  unsigned uLengthY, DiagList &DL)
	{
	if (ALPHA_Amino != g_Alpha)
		Quit("FindDiags: requires amino acid alphabet");

	DL.Clear();

	if (uLengthX < 12 || uLengthY < 12)
		return;

// Set A to shorter profile, B to longer
	const ProfPos *PA;
	const ProfPos *PB;
	unsigned uLengthA;
	unsigned uLengthB;
	bool bSwap;
	if (uLengthX < uLengthY)
		{
		bSwap = false;
		PA = PX;
		PB = PY;
		uLengthA = uLengthX;
		uLengthB = uLengthY;
		}
	else
		{
		bSwap = true;
		PA = PY;
		PB = PX;
		uLengthA = uLengthY;
		uLengthB = uLengthX;
		}

// Build tuple map for the longer profile, B
	if (uLengthB < KTUP)
		Quit("FindDiags: profile too short");

	memset(TuplePos, EMPTY, sizeof(TuplePos));

	for (unsigned uPos = 0; uPos < uLengthB - KTUP; ++uPos)
		{
		const unsigned uTuple = GetTuple(PB, uPos);
		if (EMPTY == uTuple)
			continue;
		TuplePos[uTuple] = uPos;
		}

// Find matches
	for (unsigned uPosA = 0; uPosA < uLengthA - KTUP; ++uPosA)
		{
		const unsigned uTuple = GetTuple(PA, uPosA);
		if (EMPTY == uTuple)
			continue;
		const unsigned uPosB = TuplePos[uTuple];
		if (EMPTY == uPosB)
			continue;

	// This tuple is found in both profiles
		unsigned uStartPosA = uPosA;
		unsigned uStartPosB = uPosB;

	// Try to extend the match forwards
		unsigned uEndPosA = uPosA + KTUP - 1;
		unsigned uEndPosB = uPosB + KTUP - 1;
		for (;;)
			{
			if (uLengthA - 1 == uEndPosA || uLengthB - 1 == uEndPosB)
				break;
			const unsigned uAAGroupA = PA[uEndPosA+1].m_uResidueGroup;
			if (RESIDUE_GROUP_MULTIPLE == uAAGroupA)
				break;
			const unsigned uAAGroupB = PB[uEndPosB+1].m_uResidueGroup;
			if (RESIDUE_GROUP_MULTIPLE == uAAGroupB)
				break;
			if (uAAGroupA != uAAGroupB)
				break;
			++uEndPosA;
			++uEndPosB;
			}
		uPosA = uEndPosA;

#if	TRACE
		{
		Log("Match: A %4u-%4u   ", uStartPosA, uEndPosA);
		for (unsigned n = uStartPosA; n <= uEndPosA; ++n)
			Log("%c", 'A' + PA[n].m_uResidueGroup);
		Log("\n");
		Log("       B %4u-%4u   ", uStartPosB, uEndPosB);
		for (unsigned n = uStartPosB; n <= uEndPosB; ++n)
			Log("%c", 'A' + PB[n].m_uResidueGroup);
		Log("\n");
		}
#endif

		const unsigned uLength = uEndPosA - uStartPosA + 1;
		assert(uEndPosB - uStartPosB + 1 == uLength);

		if (uLength >= g_uMinDiagLength)
			{
			if (bSwap)
				DL.Add(uStartPosB, uStartPosA, uLength);
			else
				DL.Add(uStartPosA, uStartPosB, uLength);
			}
		}
	}
Esempio n. 26
0
File: soft.c Progetto: 0x90sled/keen
////////////////////////////////////////////////////////////////////////////
//
// LoadLIBShape()
//
int LoadLIBShape(char *SLIB_Filename, char *Filename,struct Shape *SHP)
{
	#define CHUNK(Name)	(*ptr == *Name) &&			\
								(*(ptr+1) == *(Name+1)) &&	\
								(*(ptr+2) == *(Name+2)) &&	\
								(*(ptr+3) == *(Name+3))


	int RT_CODE;
	FILE *fp;
	char CHUNK[5];
	char far *ptr;
	memptr IFFfile = NULL;
	unsigned long FileLen, size, ChunkLen;
	int loop;


	RT_CODE = 1;

	// Decompress to ram and return ptr to data and return len of data in
	//	passed variable...

	if (!LoadLIBFile(SLIB_Filename,Filename,&IFFfile))
		Quit("Error Loading Compressed lib shape!");

	// Evaluate the file
	//
	ptr = MK_FP(IFFfile,0);
	if (!CHUNK("FORM"))
		goto EXIT_FUNC;
	ptr += 4;

	FileLen = *(long far *)ptr;
	SwapLong((long far *)&FileLen);
	ptr += 4;

	if (!CHUNK("ILBM"))
		goto EXIT_FUNC;
	ptr += 4;

	FileLen += 4;
	while (FileLen)
	{
		ChunkLen = *(long far *)(ptr+4);
		SwapLong((long far *)&ChunkLen);
		ChunkLen = (ChunkLen+1) & 0xFFFFFFFE;

		if (CHUNK("BMHD"))
		{
			ptr += 8;
			SHP->bmHdr.w = ((struct BitMapHeader far *)ptr)->w;
			SHP->bmHdr.h = ((struct BitMapHeader far *)ptr)->h;
			SHP->bmHdr.x = ((struct BitMapHeader far *)ptr)->x;
			SHP->bmHdr.y = ((struct BitMapHeader far *)ptr)->y;
			SHP->bmHdr.d = ((struct BitMapHeader far *)ptr)->d;
			SHP->bmHdr.trans = ((struct BitMapHeader far *)ptr)->trans;
			SHP->bmHdr.comp = ((struct BitMapHeader far *)ptr)->comp;
			SHP->bmHdr.pad = ((struct BitMapHeader far *)ptr)->pad;
			SwapWord(&SHP->bmHdr.w);
			SwapWord(&SHP->bmHdr.h);
			SwapWord(&SHP->bmHdr.x);
			SwapWord(&SHP->bmHdr.y);
			ptr += ChunkLen;
		}
		else
		if (CHUNK("BODY"))
		{
			ptr += 4;
			size = *((long far *)ptr);
			ptr += 4;
			SwapLong((long far *)&size);
			SHP->BPR = (SHP->bmHdr.w+7) >> 3;
			MM_GetPtr(&SHP->Data,size);
			if (!SHP->Data)
				goto EXIT_FUNC;
			movedata(FP_SEG(ptr),FP_OFF(ptr),FP_SEG(SHP->Data),0,size);
			ptr += ChunkLen;

			break;
		}
		else
Esempio n. 27
0
ProgNode *ProgressiveAlignE(const SeqVect &v, const Tree &GuideTree, MSA &a)
	{
	assert(GuideTree.IsRooted());

#if	TRACE
	Log("GuideTree:\n");
	GuideTree.LogMe();
#endif

	const unsigned uSeqCount = v.Length();
	const unsigned uNodeCount = 2*uSeqCount - 1;
	const unsigned uIterCount = uSeqCount - 1;

	WEIGHT *Weights = new WEIGHT[uSeqCount];
	CalcClustalWWeights(GuideTree, Weights);

	ProgNode *ProgNodes = new ProgNode[uNodeCount];

	unsigned uJoin = 0;
	unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode();
	SetProgressDesc("Align node");
	do
		{
		if (GuideTree.IsLeaf(uTreeNodeIndex))
			{
			if (uTreeNodeIndex >= uNodeCount)
				Quit("TreeNodeIndex=%u NodeCount=%u\n", uTreeNodeIndex, uNodeCount);
			ProgNode &Node = ProgNodes[uTreeNodeIndex];
			unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
			if (uId >= uSeqCount)
				Quit("Seq index out of range");
			const Seq &s = *(v[uId]);
			Node.m_MSA.FromSeq(s);
			Node.m_MSA.SetSeqId(0, uId);
			Node.m_uLength = Node.m_MSA.GetColCount();
			Node.m_Weight = Weights[uId];
		// TODO: Term gaps settable
			Node.m_Prof = ProfileFromMSA(Node.m_MSA);
			Node.m_EstringL = 0;
			Node.m_EstringR = 0;
#if	TRACE
			Log("Leaf id=%u\n", uId);
			Log("MSA=\n");
			Node.m_MSA.LogMe();
			Log("Profile (from MSA)=\n");
			ListProfile(Node.m_Prof, Node.m_uLength, &Node.m_MSA);
#endif
			}
		else
			{
			Progress(uJoin, uSeqCount - 1);
			++uJoin;

			const unsigned uMergeNodeIndex = uTreeNodeIndex;
			ProgNode &Parent = ProgNodes[uMergeNodeIndex];

			const unsigned uLeft = GuideTree.GetLeft(uTreeNodeIndex);
			const unsigned uRight = GuideTree.GetRight(uTreeNodeIndex);

			if (g_bVerbose)
				{
				Log("Align: (");
				LogLeafNames(GuideTree, uLeft);
				Log(") (");
				LogLeafNames(GuideTree, uRight);
				Log(")\n");
				}

			ProgNode &Node1 = ProgNodes[uLeft];
			ProgNode &Node2 = ProgNodes[uRight];

#if	TRACE
			Log("AlignTwoMSAs:\n");
#endif
			AlignTwoProfs(
			  Node1.m_Prof, Node1.m_uLength, Node1.m_Weight,
			  Node2.m_Prof, Node2.m_uLength, Node2.m_Weight,
			  Parent.m_Path,
			  &Parent.m_Prof, &Parent.m_uLength);
#if	TRACE_LENGTH_DELTA
			{
			unsigned L = Node1.m_uLength;
			unsigned R = Node2.m_uLength;
			unsigned P = Parent.m_Path.GetEdgeCount();
			unsigned Max = L > R ? L : R;
			unsigned d = P - Max;
			Log("LD%u;%u;%u;%u\n", L, R, P, d);
			}
#endif
			PathToEstrings(Parent.m_Path, &Parent.m_EstringL, &Parent.m_EstringR);

			Parent.m_Weight = Node1.m_Weight + Node2.m_Weight;

#if	VALIDATE
			{
#if	TRACE
			Log("AlignTwoMSAs:\n");
#endif
			PWPath TmpPath;
			AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, TmpPath);
			ProfPos *P1 = ProfileFromMSA(Node1.m_MSA, true);
			ProfPos *P2 = ProfileFromMSA(Node2.m_MSA, true);
			unsigned uLength = Parent.m_MSA.GetColCount();
			ProfPos *TmpProf = ProfileFromMSA(Parent.m_MSA, true);

#if	TRACE
			Log("Node1 MSA=\n");
			Node1.m_MSA.LogMe();

			Log("Node1 prof=\n");
			ListProfile(Node1.m_Prof, Node1.m_MSA.GetColCount(), &Node1.m_MSA);
			Log("Node1 prof (from MSA)=\n");
			ListProfile(P1, Node1.m_MSA.GetColCount(), &Node1.m_MSA);

			AssertProfsEq(Node1.m_Prof, Node1.m_uLength, P1, Node1.m_MSA.GetColCount());

			Log("Node2 prof=\n");
			ListProfile(Node2.m_Prof, Node2.m_MSA.GetColCount(), &Node2.m_MSA);

			Log("Node2 MSA=\n");
			Node2.m_MSA.LogMe();

			Log("Node2 prof (from MSA)=\n");
			ListProfile(P2, Node2.m_MSA.GetColCount(), &Node2.m_MSA);

			AssertProfsEq(Node2.m_Prof, Node2.m_uLength, P2, Node2.m_MSA.GetColCount());

			TmpPath.AssertEqual(Parent.m_Path);

			Log("Parent MSA=\n");
			Parent.m_MSA.LogMe();

			Log("Parent prof=\n");
			ListProfile(Parent.m_Prof, Parent.m_uLength, &Parent.m_MSA);

			Log("Parent prof (from MSA)=\n");
			ListProfile(TmpProf, Parent.m_MSA.GetColCount(), &Parent.m_MSA);

#endif	// TRACE
			AssertProfsEq(Parent.m_Prof, Parent.m_uLength,
			  TmpProf, Parent.m_MSA.GetColCount());
			delete[] P1;
			delete[] P2;
			delete[] TmpProf;
			}
#endif	// VALIDATE

			Node1.m_MSA.Clear();
			Node2.m_MSA.Clear();

		// Don't delete profiles, may need them for tree refinement.
			//delete[] Node1.m_Prof;
			//delete[] Node2.m_Prof;
			//Node1.m_Prof = 0;
			//Node2.m_Prof = 0;
			}
		uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex);
		}
	while (NULL_NEIGHBOR != uTreeNodeIndex);
	ProgressStepsDone();

	if (g_bBrenner)
		MakeRootMSABrenner((SeqVect &) v, GuideTree, ProgNodes, a);
	else
		MakeRootMSA(v, GuideTree, ProgNodes, a);

#if	VALIDATE
	{
	unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
	const ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];
	AssertMSAEq(a, RootProgNode.m_MSA);
	}
#endif

	delete[] Weights;
	return ProgNodes;
	}
Esempio n. 28
0
File: soft.c Progetto: 0x90sled/keen
//--------------------------------------------------------------------------
// BLoad()			-- THIS HAS NOT BEEN FULLY TESTED!
//
// NOTICE : This version of BLOAD is compatable with JAMPak V3.0 and the
//				new fileformat...
//--------------------------------------------------------------------------
unsigned long BLoad(char *SourceFile, memptr *DstPtr)
{
	int handle;

	memptr SrcPtr;
	unsigned long i, j, k, r, c;
	word flags;
	byte Buffer[8];
	unsigned long SrcLen,DstLen;
	struct CMP1Header CompHeader;
	boolean Compressed = false;


	memset((void *)&CompHeader,0,sizeof(struct CMP1Header));

	//
	// Open file to load....
	//

	if ((handle = open(SourceFile, O_RDONLY|O_BINARY)) == -1)
		return(0);

	//
	// Look for JAMPAK headers
	//

	read(handle,Buffer,4);

	if (!strncmp(Buffer,COMP,4))
	{
		//
		// Compressed under OLD file format
		//

		Compressed = true;
		SrcLen = Verify(SourceFile);

		read(handle,(void *)&CompHeader.OrginalLen,4);
		CompHeader.CompType = ct_LZW;
		MM_GetPtr(DstPtr,CompHeader.OrginalLen);
		if (!*DstPtr)
			return(0);
	}
	else
	if (!strncmp(Buffer,CMP1,4))
	{
		//
		// Compressed under new file format...
		//

		Compressed = true;
		SrcLen = Verify(SourceFile);

		read(handle,(void *)&CompHeader,sizeof(struct CMP1Header));
		MM_GetPtr(DstPtr,CompHeader.OrginalLen);
		if (!*DstPtr)
			return(0);
	}
	else
		DstLen = Verify(SourceFile);


	//
	// Load the file in memory...
	//

	if (Compressed)
	{
		DstLen = CompHeader.OrginalLen;

		if ((MM_TotalFree() < SrcLen) && (CompHeader.CompType))
		{
			if (!InitBufferedIO(handle,&lzwBIO))
				Quit("No memory for buffered I/O.");

			switch (CompHeader.CompType)
			{
				#if LZW_SUPPORT
				case ct_LZW:
					lzwDecompress(&lzwBIO,MK_FP(*DstPtr,0),CompHeader.OrginalLen,(SRC_BFILE|DEST_MEM));
				break;
				#endif

				#if LZH_SUPPORT
				case ct_LZH:
					lzhDecompress(&lzwBIO,MK_FP(*DstPtr,0),CompHeader.OrginalLen,CompHeader.CompressLen,(SRC_BFILE|DEST_MEM));
				break;
				#endif

				default:
					Quit("BLoad() - Unrecognized/Supported compression");
				break;
			}

			FreeBufferedIO(&lzwBIO);
		}
		else
		{
			CA_LoadFile(SourceFile,&SrcPtr);
			switch (CompHeader.CompType)
			{
				#if LZW_SUPPORT
				case ct_LZW:
					lzwDecompress(MK_FP(SrcPtr,8),MK_FP(*DstPtr,0),CompHeader.OrginalLen,(SRC_MEM|DEST_MEM));
				break;
				#endif

				#if LZH_SUPPORT
				case ct_LZH:
					lzhDecompress(MK_FP(SrcPtr,8),MK_FP(*DstPtr,0),CompHeader.OrginalLen,CompHeader.CompressLen,(SRC_MEM|DEST_MEM));
				break;
				#endif

				default:
					Quit("BLoad() - Unrecognized/Supported compression");
				break;
			}
			MM_FreePtr(&SrcPtr);
		}
	}
	else
		CA_LoadFile(SourceFile,DstPtr);

	close(handle);
	return(DstLen);
}
Esempio n. 29
0
char *ReadAFA(FILE *f, int *ptrSeqLength, int *ptrSeqCount)
	{
	rewind(f);
	int FileSize = GetFileSize(f);
	int BufferSize = FileSize;
	char *Buffer = all(char, BufferSize);

	char prev_c = '\n';
	bool InLabel = false;
	int Pos = 0;
	int SeqStart = 0;
	int SeqCount = 0;
	int SeqLength;

	for (;;)
		{
		int c = fgetc(f);
		if (EOF == c)
			{
			if (feof(f))
				break;
			Quit("Stream error");
			}
		if (InLabel)
			{
			if (c == '\r')
				continue;
			if ('\n' == c)
				InLabel = false;
			}
		else
			{
			if ('>' == c && '\n' == prev_c)
				{
				int ThisSeqLength = Pos - SeqStart;
				if (0 == SeqCount)
					;
				else if (1 == SeqCount)
					SeqLength = ThisSeqLength;
				else if (SeqCount > 1)
					{
					if (SeqLength != ThisSeqLength)
						Quit("ReadAFA: sequence lengths differ %d %d",
						  SeqLength, ThisSeqLength);
					}
				++SeqCount;
				SeqStart = Pos;
				InLabel = true;
				}
			else if (!isspace(c))
				{
				if (Pos >= BufferSize)
					Quit("ReadAFA: buffer too small");
				Buffer[Pos++] = (c);
				}
			}
		prev_c = c;
		}

	int ThisSeqLength = Pos - SeqStart;
	if (0 == SeqCount)
		SeqLength = ThisSeqLength;
	else
		{
		if (SeqLength != ThisSeqLength)
			Quit("ReadAFA: sequence lengths differ %d %d",
				SeqLength, ThisSeqLength);
		}

	*ptrSeqCount = SeqCount;
	*ptrSeqLength = SeqLength;

	if (Pos != SeqCount*SeqLength)
		Quit("ReadAFA: Internal error");
	return Buffer;
	}
Esempio n. 30
0
int main( int argc, char **argv )
{
    /* Flags to pass to SDL_SetVideoMode */
    int videoFlags;
    /* main loop variable */
    int done = FALSE;
    /* used to collect events */
    SDL_Event event;
    /* this holds some info about our display */
    const SDL_VideoInfo *videoInfo;
    /* whether or not the window is active */
    int isActive = TRUE;

    /* initialize SDL */
    if ( SDL_Init( SDL_INIT_VIDEO ) < 0 )
	{
	    fprintf( stderr, "Video initialization failed: %s\n",
		     SDL_GetError( ) );
	    Quit( 1 );
	}

    /* Fetch the video info */
    videoInfo = SDL_GetVideoInfo( );

    if ( !videoInfo )
	{
	    fprintf( stderr, "Video query failed: %s\n",
		     SDL_GetError( ) );
	    Quit( 1 );
	}

    /* the flags to pass to SDL_SetVideoMode */
    videoFlags  = SDL_OPENGL;          /* Enable OpenGL in SDL */
    videoFlags |= SDL_GL_DOUBLEBUFFER; /* Enable double buffering */
    videoFlags |= SDL_HWPALETTE;       /* Store the palette in hardware */
    videoFlags |= SDL_RESIZABLE;       /* Enable window resizing */

    /* This checks to see if surfaces can be stored in memory */
    if ( videoInfo->hw_available )
	videoFlags |= SDL_HWSURFACE;
    else
	videoFlags |= SDL_SWSURFACE;

    /* This checks if hardware blits can be done */
    if ( videoInfo->blit_hw )
	videoFlags |= SDL_HWACCEL;

    /* Sets up OpenGL double buffering */
    SDL_GL_SetAttribute( SDL_GL_DOUBLEBUFFER, 1 );

    /* get a SDL surface */
    surface = SDL_SetVideoMode( SCREEN_WIDTH, SCREEN_HEIGHT, SCREEN_BPP,
				videoFlags );

    /* Verify there is a surface */
    if ( !surface )
	{
	    fprintf( stderr,  "Video mode set failed: %s\n", SDL_GetError( ) );
	    Quit( 1 );
	}

    /* initialize OpenGL */
    initGL( );

    /* resize the initial window */
    resizeWindow( SCREEN_WIDTH, SCREEN_HEIGHT );

    /* wait for events */ 
    while ( !done )
	{
	    /* handle the events in the queue */

	    while ( SDL_PollEvent( &event ) )
		{
		    switch( event.type )
			{
			case SDL_ACTIVEEVENT:
			    /* Something's happend with our focus
			     * If we lost focus or we are iconified, we
			     * shouldn't draw the screen
			     */
			    if ( event.active.gain == 0 )
				isActive = FALSE;
			    else
				isActive = TRUE;
			    break;			    
			case SDL_VIDEORESIZE:
#if 0
			    /* handle resize event */
			    surface = SDL_SetVideoMode( event.resize.w,
							event.resize.h,
							16, videoFlags );
			    if ( !surface )
				{
				    fprintf( stderr, "Could not get a surface after resize: %s\n", SDL_GetError( ) );
				    Quit( 1 );
				}
			    resizeWindow( event.resize.w, event.resize.h );
#endif
			    break;
			case SDL_KEYDOWN:
			    /* handle key presses */
			    handleKeyPress( &event.key.keysym );
			    break;
			case SDL_QUIT:
			    /* handle quit requests */
			    done = TRUE;
			    break;
			default:
			    break;
			}
		}

	    /* draw the scene */
	    if ( isActive )
		drawGLScene( );
	}

    /* clean ourselves up and exit */
    Quit( 0 );

    /* Should never get here */
    return( 0 );
}