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();

//.........这里部分代码省略.........

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
//.........这里部分代码省略.........

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;
	}
}

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;
	}
//.........这里部分代码省略.........

void
EventQueue::OnSignal(int signo)
{
  Quit();
}

void QuitEmulator(void)
{
	Quit();
}

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
}

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);
//.........这里部分代码省略.........

//.........这里部分代码省略.........

#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;
	}

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
//.........这里部分代码省略.........

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);
	}

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

  //
  // 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();
    }
  }

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
//.........这里部分代码省略.........

void
UrlWrapper::ReadyToRun(void)
{
	Quit();
}

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
//.........这里部分代码省略.........

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);
//.........这里部分代码省略.........

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;
//.........这里部分代码省略.........

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)
							{
//.........这里部分代码省略.........

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