NAMESPACE_UPP
CH_STYLE(MultiButton, Style, StyleDefault)
{
for(int i = 0; i < 4; i++) {
simple[i] = left[i] = right[i] = lmiddle[i] = rmiddle[i]
= Button::StyleEdge().look[i];
monocolor[i] = Button::StyleEdge().monocolor[i];
fmonocolor[i] = i == 3 ? SColorDisabled() : SColorText();
look[i] = trivial[i] = ChLookWith(simple[i], CtrlsImg::DA(), monocolor[i]);
edge[i] = EditFieldEdge();
}
activeedge = false;
trivialborder = DPI(1);
border = DPI(1);
pressoffset = Button::StyleEdge().pressoffset;
sep1 = SColorHighlight();
sep2 = SColorLight();
sepm = DPI(2);
stdwidth = FrameButtonWidth();
trivialsep = false;
margin = Rect(DPI(2), 2, DPI(2), 2);
usetrivial = false;
overpaint = loff = roff = 0;
error = Blend(LtRed(), Red());
}
void CTrafficMonitorApp::DPI(CRect & rect)
{
rect.left = DPI(rect.left);
rect.right = DPI(rect.right);
rect.top = DPI(rect.top);
rect.bottom = DPI(rect.bottom);
}
FileList::FileList() {
iconwidth = DPI(16);
ItemHeight(max(Draw::GetStdFontCy(), DPI(17)));
Ctrl::Add(edit);
edit.Hide();
edit.SetFrame(BlackFrame());
renaming = false;
justname = false;
accelkey = false;
selectdir = false;
SetDisplay(*this);
}
Size MakeLogo(Ctrl& parent, Array<Ctrl>& ctrl)
{
Image logo = IdeImg::logo();
Size isz = logo.GetSize();
ImageCtrl& l = ctrl.Create<ImageCtrl>();
Label& v1 = ctrl.Create<Label>();
l.SetImage(logo);
Size sz = Size(isz.cx, isz.cy/* + 80*/);
const CppBase& cpp = CodeBase();
int total = 0;
for(int i = 0; i < cpp.GetCount(); i++)
total += cpp[i].GetCount();
String h;
#ifdef bmSVN_REVISION
h << "Version " << bmSVN_REVISION;
#else
h << "Version " << IDE_VERSION;
#endif
if(sizeof(void *) == 8)
h << "\n(64 bit)";
else
h << "\n(32 bit)";
#ifdef _MSC_VER
h << " (MSC)";
#endif
#if __GNUC__
#if __clang__
h << " (CLANG)";
#else
h << " (GCC)";
#endif
#endif
#if __cplusplus >= 201100
h << " (C++11)";
#endif
#ifdef GUI_GTK
h << " (Gtk)";
#endif
h << "\n";
#ifdef bmTIME
h << "Compiled " << bmTIME << "\n";
#endif
h << "Using " << MemoryUsedKb() << " KB\n";
if(cpp.GetCount())
h << "CodeBase: " << cpp.GetCount() << " classes, " << total << " items\n";
v1 = h;
v1.HSizePos(DPI(220), DPI(10)).BottomPos(DPI(20), Arial(DPI(20)).GetHeight() * 5);
v1.SetFont(Arial(DPI(10)));
l.Add(v1);
parent.Add(ctrl.Create<StaticRect>().Color(White).SizePos());
parent.Add(l.TopPos(0, isz.cy).LeftPos(0, isz.cx));
return sz;
}
void PLBmpDecoder::Open (PLDataSource * pDataSrc)
{
m_pBMI = getInfoHeader (pDataSrc, &m_Pal[0]);
PLPixelFormat pf;
if (m_pBMI->biBitCount <= 8) {
pf = PLPixelFormat::L8;
} else {
if (m_pBMI->biBitCount == 32) {
pf = PLPixelFormat::A8R8G8B8;
} else {
pf = PLPixelFormat::X8R8G8B8;
}
}
PLPoint DPI(0,0);
if (m_pBMI->biXPelsPerMeter > 0)
DPI.x = (int)((float)m_pBMI->biXPelsPerMeter / 39.37f+0.5);
if (DPI.x <= 1)
DPI.x = 0;
if (m_pBMI->biYPelsPerMeter > 0)
DPI.y = (int)((float)m_pBMI->biYPelsPerMeter / 39.37f+0.5);
if (DPI.y <= 1)
DPI.y = 0;
SetBmpInfo (PLPoint (m_pBMI->biWidth, m_pBMI->biHeight),
DPI, pf);
}
void WorkspaceWork::SyncErrorPackages()
{
for(int i = 0; i < package.GetCount(); i++) {
FileList::File f = package.Get(i);
if(!IsAux(f.name) && i < speed.GetCount()) {
FileList::File ff = f;
String path = GetFileFolder(PackagePath(f.name));
#ifdef PLATFORM_WIN32
path = ToLower(path);
#endif
ff.icon = i ? IdeImg::Package() : IdeImg::MainPackage();
if(speed[i])
ff.icon = ImageOver(ff.icon, IdeImg::FastPackage());
ff.underline = Null;
for(int q = 0; q < errorfiles.GetCount(); q++) {
if(errorfiles[q].StartsWith(path)) {
ff.icon = ImageOverRed(ff.icon);
ff.underline = LtRed;
break;
}
}
ff.icon = DPI(ff.icon);
package.Set(i, ff);
}
}
}
CH_STYLE(MenuBar, Style, StyleDefault)
{
topitem[0] = Null;
topitem[1] = topitem[2] = item = SColorHighlight();
topitemtext[0] = menutext = SColorMenuText();
topitemtext[1] = topitemtext[2] = itemtext = SColorHighlightText();
topbar = SColorFace();
maxiconsize = Size(16, 16);
arealook = Null;
look = SColorFace();
separator = breaksep = SeparatorCtrl::StyleDefault();
ImageBuffer ib(7, 7);
Fill(ib, SColorShadow(), 7 * 7);
for(int i = 0; i < 5; i++)
Fill(ib[i + 1] + 1, SColorMenu(), 5);
ib.SetHotSpot(Point(3, 3));
ib.Set2ndSpot(Point(3, 3));
popupframe = Image(ib);
popupbody = SColorMenu();
popupiconbar = Null;
leftgap = DPI(16) + Zx(4);
textgap = Zx(3);
lsepm = rsepm = Zx(2);
pullshift.x = 0;
pullshift.y = -1;
}
AboutDlg() {
Size isz = MakeLogo(*this, ctrl);
int cx = min(isz.cx * 2, GetWorkArea().GetWidth());
SetRect(0, 0, cx, isz.cy);
about.SetQTF(GetTopic("ide/app/About$en-us"), Zoom(DPI(120), 1024));
about.SetZoom(Zoom(1, 1));
about.RightPos(0, cx - isz.cx - DPI(1)).VSizePos();
about.HMargins(Zx(4));
about.SetFrame(NullFrame());
about.NoLazy();
Background(PaintRect(ColorDisplay(), SColorPaper()));
Add(about);
// separator.Color(Gray());
// Add(separator.RightPos(cx - isz.cx, DPI(1)).VSizePos());
Title("About TheIDE");
}
void MultiButton::SyncInfo()
{
if((HasMouse() || info.HasMouse()) && display &&
(GetMouseFlags() & (K_MOUSELEFT|K_MOUSERIGHT|K_MOUSEMIDDLE)) == 0) {
Point p = GetMouseViewPos();
NilDraw nw;
Rect r = Paint0(nw, true);
if(r.Contains(p)) {
Value v = convert->Format(value);
int cm = DPI(2);
r.left -= cm;
r.right += cm;
info.Set(this, r, value, display, SColorText, SColorPaper, 0, DPI(2));
return;
}
}
info.Cancel();
}
virtual void Paint(Draw& w, const Rect& r, const Value& q, Color ink, Color paper, dword style) const {
ValueArray va = q;
String txt = va[0];
Image icon = va[1];
if(IsNull(icon))
icon = IdeImg::Package();
else
icon = DPI(icon, 16);
w.DrawRect(r, paper);
w.DrawImage(r.left, r.top + (r.Height() - icon.GetHeight()) / 2, icon);
w.DrawText(r.left + Zx(20), r.top + (r.Height() - Draw::GetStdFontCy()) / 2, txt, fnt, ink);
}
Rect MultiButton::Paint0(Draw& w, bool getcr)
{
Size sz = GetSize();
int border, lx, rx;
bool frm = Metrics(border, lx, rx);
int mst = ChState(MAIN);
if(frm && !nobg && !getcr)
ChPaint(w, sz, style->edge[style->activeedge ? mst : 0]);
bool left = false;
bool right = false;
for(int i = 0; i < button.GetCount(); i++) {
SubButton& b = button[i];
int st = ChState(i);
int x = 0, cx = 0;
GetPos(b, lx, rx, x, cx);
if(getcr)
continue;
bool dopaint = true;
Value v = b.left ? left ? style->lmiddle[st] : style->left[st]
: right ? style->rmiddle[st] : style->right[st];
if(!nobg) {
if(ComplexFrame())
ChPaint(w, x, border, cx, sz.cy - 2 * border, style->simple[st]);
else
if(frm) {
if(IsTrivial() && style->usetrivial)
dopaint = false;
ChPaint(w, x, border, cx, sz.cy - 2 * border,
dopaint ? v : style->trivial[st]);
}
else {
w.Clip(x, 0, cx, sz.cy);
ChPaint(w, sz, style->look[Frame() ? mst : st]);
if(IsNull(v) || !Frame()) {
if((!IsTrivial() || style->trivialsep) && IsEnabled()) {
if(b.left) {
if(left)
ChPaint(w, x, style->sepm, 1, sz.cy - 2 * style->sepm, style->sep1);
ChPaint(w, x + cx - 1, style->sepm, 1, sz.cy - 2 * style->sepm, style->sep2);
}
else {
ChPaint(w, x, style->sepm, 1, sz.cy - 2 * style->sepm, style->sep1);
if(right)
ChPaint(w, x + cx - 1, style->sepm, 1, sz.cy - 2 * style->sepm, style->sep2);
}
}
}
else
ChPaint(w, x, 0, cx, sz.cy, v);
w.End();
}
}
if(dopaint) {
Size tsz = GetTextSize(b.label, StdFont());
Image m = tsz.cx > 0 ? b.img : (Image)Nvl(b.img, CtrlsImg::DA());
Size isz = m.GetSize();
Point p = (st == CTRL_PRESSED) * style->pressoffset;
p.x += x + (cx - isz.cx - tsz.cx - (tsz.cx > 0 && isz.cx > 0 ? LB_IMAGE : 0)) / 2;
p.y += (sz.cy - isz.cy) / 2;
if(b.left) {
if(!left) p.x += style->loff;
}
else
if(!right) p.x += style->roff;
if(b.monoimg || IsNull(b.img))
w.DrawImage(p.x, p.y, m, frm ? style->fmonocolor[st] : style->monocolor[st]);
else
w.DrawImage(p.x, p.y, m);
if(tsz.cx > 0) {
if(isz.cx > 0)
p.x += isz.cx + LB_IMAGE;
w.DrawText(p.x, (sz.cy - tsz.cy) / 2, b.label);
}
}
(b.left ? left : right) = true;
}
Rect r, cr;
cr = GetSize();
cr.left = lx;
cr.right = rx;
Color text = SColorLabel();
Color paper = Null;
if(!nobg) {
if(ComplexFrame()) {
r = cr;
paper = HasFocus() ? SColorHighlight() : SColorPaper();
if(HasFocus())
text = SColorHighlightText();
w.DrawRect(r, paper);
}
else
if(frm) {
Rect m = GetMargin();
r = Rect(max(lx, m.left), m.top, min(rx, sz.cx - m.right), sz.cy - m.bottom);
Color paper;
if(mst == CTRL_HOT && !IsTrivial())
paper = Blend(SColorHighlight, SColorPaper, 235);
else
if(mst == CTRL_PRESSED && !IsTrivial())
paper = Blend(SColorHighlight, SColorFace, 235);
else
if(HasFocus()) {
paper = SColorHighlight();
text = SColorHighlightText();
}
else
paper = SColorPaper();
w.DrawRect(r, paper);
cr = r;
}
else {
w.Clip(lx, 0, rx - lx, sz.cy);
ChPaint(w, sz, style->look[mst]);
Rect m = style->margin;
r = Rect(max(lx, m.left), m.top, min(rx, sz.cx - m.right), sz.cy - m.bottom);
if(!IsTrivial() || style->trivialsep) {
if(left) {
r.left++;
if(IsEnabled())
ChPaint(w, lx, style->sepm, 1, sz.cy - 2 * style->sepm, style->sep1);
}
if(right) {
if(IsEnabled())
ChPaint(w, rx - 1, style->sepm, 1, sz.cy - 2 * style->sepm, style->sep2);
r.right--;
}
}
w.End();
cr = r;
}
}
cr.left += DPI(1);
Rect clr = cr;
if(!IsNull(valuecy) && cr.GetHeight() > valuecy) {
cr.top += (cr.GetHeight() - valuecy) / 2;
cr.bottom = cr.top + valuecy;
}
if(getcr)
return cr;
Value v = convert->Format(value);
bool f = HasFocus() && !push && frm;
if(cr.left < cr.right && display) {
w.Clip(clr);
if(!IsNull(error)) {
v = error;
text = style->error;
}
display->Paint(w, cr, v,
IsShowEnabled() ? text : SColorDisabled,
paper, f ? Display::CURSOR : Display::FOCUS|Display::CURSOR);
w.End();
}
if(!frm && HasFocus())
DrawFocus(w, r);
return cr;
}
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;
}
static SCORE TraceBackDimer( const SCORE *DPM_, const SCORE *DPD_, const SCORE *DPI_,
const char *TBM_, const char *TBD_, const char *TBI_,
unsigned uLengthA, unsigned uLengthB, PWPath &Path)
{
const unsigned uPrefixCountA = uLengthA + 1;
unsigned uPrefixLengthA = uLengthA;
unsigned uPrefixLengthB = uLengthB;
char cEdge = 'M';
SCORE scoreMax = DPM(uLengthA, uLengthB);
if (DPD(uLengthA, uLengthB) > scoreMax)
{
scoreMax = DPD(uLengthA, uLengthB);
cEdge = 'D';
}
if (DPI(uLengthA, uLengthB) > scoreMax)
{
scoreMax = DPI(uLengthA, uLengthB);
cEdge = 'I';
}
for (;;)
{
if (0 == uPrefixLengthA && 0 == uPrefixLengthB)
break;
PWEdge Edge;
Edge.cType = cEdge;
Edge.uPrefixLengthA = uPrefixLengthA;
Edge.uPrefixLengthB = uPrefixLengthB;
Path.PrependEdge(Edge);
#if TRACE
Log("PLA=%u PLB=%u Edge=%c\n", uPrefixLengthA, uPrefixLengthB, cEdge);
#endif
switch (cEdge)
{
case 'M':
assert(uPrefixLengthA > 0 && uPrefixLengthB > 0);
cEdge = TBM(uPrefixLengthA, uPrefixLengthB);
--uPrefixLengthA;
--uPrefixLengthB;
break;
case 'D':
assert(uPrefixLengthA > 0);
cEdge = TBD(uPrefixLengthA, uPrefixLengthB);
--uPrefixLengthA;
break;
case 'I':
assert(uPrefixLengthB > 0);
cEdge = TBI(uPrefixLengthA, uPrefixLengthB);
--uPrefixLengthB;
break;
default:
Quit("Invalid edge PLA=%u PLB=%u %c", uPrefixLengthA, uPrefixLengthB, cEdge);
}
}
#if TRACE
Path.LogMe();
#endif
return scoreMax;
}
SCORE SW(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 *DPM_ = new SCORE[LM];
SCORE *DPD_ = new SCORE[LM];
SCORE *DPI_ = new SCORE[LM];
DPM(0, 0) = 0;
DPD(0, 0) = MINUS_INFINITY;
DPI(0, 0) = MINUS_INFINITY;
DPM(1, 0) = MINUS_INFINITY;
DPD(1, 0) = MINUS_INFINITY;
DPI(1, 0) = MINUS_INFINITY;
DPM(0, 1) = MINUS_INFINITY;
DPD(0, 1) = MINUS_INFINITY;
DPI(0, 1) = MINUS_INFINITY;
// Empty prefix of B is special case
for (unsigned uPrefixLengthA = 2; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
{
// M=LetterA+LetterB, impossible with empty prefix
DPM(uPrefixLengthA, 0) = MINUS_INFINITY;
// D=LetterA+GapB, never optimal in local alignment with gap penalties
DPD(uPrefixLengthA, 0) = MINUS_INFINITY;
// I=GapA+LetterB, impossible with empty prefix
DPI(uPrefixLengthA, 0) = MINUS_INFINITY;
}
// Empty prefix of A is special case
for (unsigned uPrefixLengthB = 2; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
{
// M=LetterA+LetterB, impossible with empty prefix
DPM(0, uPrefixLengthB) = MINUS_INFINITY;
// D=LetterA+GapB, impossible with empty prefix
DPD(0, uPrefixLengthB) = MINUS_INFINITY;
// I=GapA+LetterB, never optimal in local alignment with gap penalties
DPI(0, uPrefixLengthB) = MINUS_INFINITY;
}
SCORE scoreMax = MINUS_INFINITY;
unsigned uPrefixLengthAMax = uInsane;
unsigned uPrefixLengthBMax = uInsane;
// ============
// Main DP loop
// ============
SCORE scoreGapCloseB = MINUS_INFINITY;
for (unsigned uPrefixLengthB = 1; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
{
const ProfPos &PPB = PB[uPrefixLengthB - 1];
SCORE scoreGapCloseA = MINUS_INFINITY;
for (unsigned uPrefixLengthA = 1; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
{
const ProfPos &PPA = PA[uPrefixLengthA - 1];
{
// Match M=LetterA+LetterB
SCORE scoreLL = ScoreProfPos2(PPA, PPB);
SCORE scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1);
SCORE scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseA;
SCORE scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + scoreGapCloseB;
SCORE scoreBest;
if (scoreMM >= scoreDM && scoreMM >= scoreIM)
scoreBest = scoreMM;
else if (scoreDM >= scoreMM && scoreDM >= scoreIM)
scoreBest = scoreDM;
else
{
assert(scoreIM >= scoreMM && scoreIM >= scoreDM);
scoreBest = scoreIM;
}
if (scoreBest < 0)
scoreBest = 0;
scoreBest += scoreLL;
if (scoreBest > scoreMax)
{
scoreMax = scoreBest;
uPrefixLengthAMax = uPrefixLengthA;
uPrefixLengthBMax = uPrefixLengthB;
}
DPM(uPrefixLengthA, uPrefixLengthB) = scoreBest;
}
{
// Delete D=LetterA+GapB
SCORE scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) +
PA[uPrefixLengthA-1].m_scoreGapOpen;
SCORE scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB);
SCORE scoreBest;
if (scoreMD >= scoreDD)
scoreBest = scoreMD;
else
{
assert(scoreDD >= scoreMD);
scoreBest = scoreDD;
}
DPD(uPrefixLengthA, uPrefixLengthB) = scoreBest;
}
// Insert I=GapA+LetterB
{
SCORE scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) +
PB[uPrefixLengthB - 1].m_scoreGapOpen;
SCORE scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1);
SCORE scoreBest;
if (scoreMI >= scoreII)
scoreBest = scoreMI;
else
{
assert(scoreII > scoreMI);
scoreBest = scoreII;
}
DPI(uPrefixLengthA, uPrefixLengthB) = scoreBest;
}
scoreGapCloseA = PPA.m_scoreGapClose;
}
scoreGapCloseB = PPB.m_scoreGapClose;
}
#if TRACE
Log("DPM:\n");
ListDP(DPM_, PA, PB, uPrefixLengthA, uPrefixLengthB);
Log("DPD:\n");
ListDP(DPD_, PA, PB, uPrefixLengthA, uPrefixLengthB);
Log("DPI:\n");
ListDP(DPI_, PA, PB, uPrefixLengthA, uPrefixLengthB);
#endif
assert(scoreMax == DPM(uPrefixLengthAMax, uPrefixLengthBMax));
TraceBackSW(PA, uLengthA, PB, uLengthB, DPM_, DPD_, DPI_,
uPrefixLengthAMax, uPrefixLengthBMax, Path);
#if TRACE
SCORE scorePath = FastScorePath2(PA, uLengthA, PB, uLengthB, Path);
Path.LogMe();
Log("Score = %s Path = %s\n", LocalScoreToStr(scoreMax), LocalScoreToStr(scorePath));
#endif
delete[] DPM_;
delete[] DPD_;
delete[] DPI_;
return scoreMax;
}
/**
* @brief Initializes main window.
*/
MainFrame::MainFrame()
:wxFrame(NULL,wxID_ANY,wxT("UltraDefrag"))
{
g_mainFrame = this;
m_vList = NULL;
m_cMap = NULL;
m_currentJob = NULL;
m_busy = false;
m_paused = false;
// set main window icon
SetIcons(wxICON(appicon));
// read configuration
ReadAppConfiguration();
ProcessCommandEvent(ID_ReadUserPreferences);
// set main window title
wxString *instdir = new wxString();
//genBTC re-arranged the below, A LOT.
wxStandardPaths stdpaths;
wxFileName exepath(stdpaths.GetExecutablePath());
wxString cd = exepath.GetPath();
if((wxGetEnv(wxT("UD_INSTALL_DIR"),instdir))&&(cd.CmpNoCase(*instdir) == 0)) {
itrace("current directory matches installation location, so it isn't portable");
itrace("installation location: %ls",instdir->wc_str());
m_title = new wxString(wxT(VERSIONINTITLE));
} else {
itrace("current directory differs from installation location, so it is portable");
itrace("current directory: %ls",cd.wc_str());
wxSetEnv(wxT("UD_IS_PORTABLE"),wxT("1"));
m_title = new wxString(wxT(VERSIONINTITLE_PORTABLE));
}
//genBTC re-arranged the above, A LOT.
ProcessCommandEvent(ID_SetWindowTitle);
delete instdir;
// set main window size and position
SetSize(m_width,m_height);
if(!m_saved){
CenterOnScreen();
GetPosition(&m_x,&m_y);
}
Move(m_x,m_y);
if(m_maximized) Maximize(true);
SetMinSize(wxSize(DPI(MAIN_WINDOW_MIN_WIDTH),DPI(MAIN_WINDOW_MIN_HEIGHT)));
// create menu, tool and status bars
InitMenu(); InitToolbar(); InitStatusBar();
//make sizer1 to hold the the tabbed "notebook". And make the notebook
wxBoxSizer* bSizer1;
bSizer1 = new wxBoxSizer( wxVERTICAL );
m_notebook1 = new wxNotebook( this, wxID_ANY, wxDefaultPosition, wxDefaultSize, 0 );
//make a panel inside the notebook to hold the m_splitter
m_panel1 = new wxPanel( m_notebook1, wxID_ANY, wxDefaultPosition, wxDefaultSize, wxTAB_TRAVERSAL );
// create list of volumes and cluster map (with splitter as parent)
m_splitter = new wxSplitterWindow(m_panel1,wxID_ANY, wxDefaultPosition,wxDefaultSize,
wxSP_3D | wxCLIP_CHILDREN);
m_splitter->SetMinimumPaneSize(DPI(MIN_PANEL_HEIGHT));
m_vList = new DrivesList(m_splitter,wxLC_REPORT | wxLC_NO_SORT_HEADER |
wxLC_HRULES | wxLC_VRULES | wxBORDER_NONE);
m_cMap = new ClusterMap(m_splitter);
m_splitter->SplitHorizontally(m_vList,m_cMap);
int height = GetClientSize().GetHeight();
int maxPanelHeight = height - DPI(MIN_PANEL_HEIGHT) - m_splitter->GetSashSize();
if(m_separatorPosition < DPI(MIN_PANEL_HEIGHT)) m_separatorPosition = DPI(MIN_PANEL_HEIGHT);
else if(m_separatorPosition > maxPanelHeight) m_separatorPosition = maxPanelHeight;
m_splitter->SetSashPosition(m_separatorPosition);
// update frame layout so we'll be able to initialize
// list of volumes and cluster map properly
wxSizeEvent evt(wxSize(m_width,m_height));
ProcessEvent(evt); m_splitter->UpdateSize();
InitVolList();
m_vList->SetFocus();
// populate list of volumes
m_listThread = new ListThread();
//make sizer2 to Fit the splitter, and initialize it.
wxBoxSizer* bSizer2;
bSizer2 = new wxBoxSizer( wxVERTICAL );
bSizer2->Add( m_splitter, 1, wxEXPAND, 1 );
m_panel1->SetSizer( bSizer2 );
//Finish Tab1 - Add the Panel1(Splitter+sizer2) to the notebook.
m_notebook1->AddPage( m_panel1, wxT("Drives"), false );
//make a 2nd panel inside the notebook to hold the 2nd page(a grid)
m_panel2 = new wxPanel( m_notebook1, wxID_ANY, wxDefaultPosition, wxDefaultSize, wxTAB_TRAVERSAL );
m_filesList = new FilesList(m_panel2,wxLC_REPORT /* | wxLC_SINGLE_SEL | wxLC_NO_SORT_HEADER*/ \
| wxLC_VIRTUAL | wxLC_HRULES | wxLC_VRULES | wxBORDER_NONE);
InitFilesList();
//make sizer3 to Fit the page2list, and initialize it.
wxBoxSizer* bSizer3;
bSizer3 = new wxBoxSizer( wxVERTICAL );
bSizer3->Add( m_filesList, 1, wxEXPAND, 1 );
m_panel2->SetSizer( bSizer3 );
bSizer3->Fit( m_panel2 );
//Finish Tab 2 - Add the Panel2(page2list+sizer3) to the notebook.
m_notebook1->AddPage( m_panel2, wxT("Files"), false );
//Finish Notebook & initialize
bSizer1->Add( m_notebook1, 1, wxEXPAND, 1 );
this->SetSizer( bSizer1 );
// check the boot time defragmenter presence
wxFileName btdFile(wxT("%SystemRoot%\\system32\\defrag_native.exe"));
btdFile.Normalize();
bool btd = btdFile.FileExists();
m_menuBar->FindItem(ID_BootEnable)->Enable(btd);
m_menuBar->FindItem(ID_BootScript)->Enable(btd);
m_toolBar->EnableTool(ID_BootEnable,btd);
m_toolBar->EnableTool(ID_BootScript,btd);
if(btd && ::winx_bootex_check(L"defrag_native") > 0){
m_menuBar->FindItem(ID_BootEnable)->Check(true);
m_toolBar->ToggleTool(ID_BootEnable,true);
m_btdEnabled = true;
} else {
m_btdEnabled = false;
}
// launch threads for time consuming operations
m_btdThread = btd ? new BtdThread() : NULL;
m_configThread = new ConfigThread();
m_crashInfoThread = new CrashInfoThread();
wxConfigBase *cfg = wxConfigBase::Get();
int ulevel = (int)cfg->Read(wxT("/Upgrade/Level"),1);
wxMenuItem *item = m_menuBar->FindItem(ID_HelpUpgradeNone + ulevel);
if(item) item->Check();
m_upgradeThread = new UpgradeThread(ulevel);
// set system tray icon
m_systemTrayIcon = new SystemTrayIcon();
if(!m_systemTrayIcon->IsOk()){
etrace("system tray icon initialization failed");
wxSetEnv(wxT("UD_MINIMIZE_TO_SYSTEM_TRAY"),wxT("0"));
}
SetSystemTrayIcon(wxT("tray"),wxT("UltraDefrag"));
// set localized text
ProcessCommandEvent(ID_LocaleChange + g_locale->GetLanguage());
// allow disk processing
m_jobThread = new JobThread();
//create query thread to perform queries without blocking the GUI
//(sort of like jobs) - may not be good to have both possibly running at once.
//Create Query Tab, Tab #3.
InitQueryMenu();
UD_DisableTool(ID_Stop); //change stop icon to be not always enabled.
}
SCORE TraceBack(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, const SCORE *DPM_, const SCORE *DPD_, const SCORE *DPI_,
PWPath &Path)
{
#if TRACE
Log("\n");
Log("TraceBack LengthA=%u LengthB=%u\n", uLengthA, uLengthB);
#endif
assert(uLengthB > 0 && uLengthA > 0);
const unsigned uPrefixCountA = uLengthA + 1;
const unsigned uPrefixCountB = uLengthB + 1;
Path.Clear();
unsigned uPrefixLengthA = uLengthA;
unsigned uPrefixLengthB = uLengthB;
const SCORE scoreM = DPM(uPrefixLengthA, uPrefixLengthB);
SCORE scoreD = DPD(uPrefixLengthA, uPrefixLengthB);
SCORE scoreI = DPI(uPrefixLengthA, uPrefixLengthB);
const ProfPos &LastPPA = PA[uLengthA - 1];
const ProfPos &LastPPB = PB[uLengthB - 1];
scoreD += LastPPA.m_scoreGapClose;
scoreI += LastPPB.m_scoreGapClose;
char cEdgeType = cInsane;
SCORE scoreMax;
if (scoreM >= scoreD && scoreM >= scoreI)
{
scoreMax = scoreM;
cEdgeType = 'M';
}
else if (scoreD >= scoreM && scoreD >= scoreI)
{
scoreMax = scoreD;
cEdgeType = 'D';
}
else
{
assert(scoreI >= scoreM && scoreI >= scoreD);
scoreMax = scoreI;
cEdgeType = 'I';
}
for (;;)
{
if ('S' == cEdgeType)
break;
PWEdge Edge;
Edge.cType = cEdgeType;
Edge.uPrefixLengthA = uPrefixLengthA;
Edge.uPrefixLengthB = uPrefixLengthB;
Path.PrependEdge(Edge);
char cPrevEdgeType;
unsigned uPrevPrefixLengthA = uPrefixLengthA;
unsigned uPrevPrefixLengthB = uPrefixLengthB;
switch (cEdgeType)
{
case 'M':
{
assert(uPrefixLengthA > 0);
assert(uPrefixLengthB > 0);
const ProfPos &PPA = PA[uPrefixLengthA - 1];
const ProfPos &PPB = PB[uPrefixLengthB - 1];
const SCORE Score = DPM(uPrefixLengthA, uPrefixLengthB);
const SCORE scoreMatch = ScoreProfPos2(PPA, PPB);
SCORE scoreSM;
if (1 == uPrefixLengthA && 1 == uPrefixLengthB)
scoreSM = scoreMatch;
else
scoreSM = MINUS_INFINITY;
SCORE scoreMM = MINUS_INFINITY;
SCORE scoreDM = MINUS_INFINITY;
SCORE scoreIM = MINUS_INFINITY;
if (uPrefixLengthA > 1 && uPrefixLengthB > 1)
scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1) + scoreMatch;
if (uPrefixLengthA > 1)
{
SCORE scoreTransDM = PA[uPrefixLengthA-2].m_scoreGapClose;
scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + scoreTransDM + scoreMatch;
}
if (uPrefixLengthB > 1)
{
SCORE scoreTransIM = PB[uPrefixLengthB-2].m_scoreGapClose;
scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + scoreTransIM + scoreMatch;
}
if (EQ(scoreMM, Score))
cPrevEdgeType = 'M';
else if (EQ(scoreDM, Score))
cPrevEdgeType = 'D';
else if (EQ(scoreIM, Score))
cPrevEdgeType = 'I';
else if (EQ(scoreSM, Score))
cPrevEdgeType = 'S';
else
Quit("TraceBack: failed to match M score=%g M=%g D=%g I=%g S=%g",
Score, scoreMM, scoreDM, scoreIM, scoreSM);
--uPrevPrefixLengthA;
--uPrevPrefixLengthB;
break;
}
case 'D':
{
assert(uPrefixLengthA > 0);
const SCORE Score = DPD(uPrefixLengthA, uPrefixLengthB);
SCORE scoreMD = MINUS_INFINITY;
SCORE scoreDD = MINUS_INFINITY;
SCORE scoreSD = MINUS_INFINITY;
if (uPrefixLengthB == 0)
{
if (uPrefixLengthA == 1)
scoreSD = PA[0].m_scoreGapOpen;
else
scoreSD = DPD(uPrefixLengthA - 1, 0);
}
if (uPrefixLengthA > 1)
{
const ProfPos &PPA = PA[uPrefixLengthA - 1];
SCORE scoreTransMD = PPA.m_scoreGapOpen;
scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) + scoreTransMD;
scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB);
}
if (EQ(Score, scoreMD))
cPrevEdgeType = 'M';
else if (EQ(Score, scoreDD))
cPrevEdgeType = 'D';
else if (EQ(Score, scoreSD))
cPrevEdgeType = 'S';
else
Quit("TraceBack: failed to match D");
--uPrevPrefixLengthA;
break;
}
case 'I':
{
assert(uPrefixLengthB > 0);
const SCORE Score = DPI(uPrefixLengthA, uPrefixLengthB);
SCORE scoreMI = MINUS_INFINITY;
SCORE scoreII = MINUS_INFINITY;
SCORE scoreSI = MINUS_INFINITY;
if (uPrefixLengthA == 0)
{
if (uPrefixLengthB == 1)
scoreSI = PB[0].m_scoreGapOpen;
else
scoreSI = DPI(0, uPrefixLengthB - 1);
}
if (uPrefixLengthB > 1)
{
const ProfPos &PPB = PB[uPrefixLengthB - 1];
SCORE scoreTransMI = PPB.m_scoreGapOpen;
scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) + scoreTransMI;
scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1);
}
if (EQ(Score, scoreMI))
cPrevEdgeType = 'M';
else if (EQ(Score, scoreII))
cPrevEdgeType = 'I';
else if (EQ(Score, scoreSI))
cPrevEdgeType = 'S';
else
Quit("TraceBack: failed to match I");
--uPrevPrefixLengthB;
break;
}
default:
assert(false);
}
#if TRACE
Log("Edge %c%c%u.%u", cPrevEdgeType, cEdgeType, uPrefixLengthA, uPrefixLengthB);
Log("\n");
#endif
cEdgeType = cPrevEdgeType;
uPrefixLengthA = uPrevPrefixLengthA;
uPrefixLengthB = uPrevPrefixLengthB;
}
return scoreMax;
}
// Global alignment dynamic programming
// This variant optimizes the profile-profile SP score under the
// dimer approximation.
SCORE GlobalAlignDimer(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 *DPM_ = new SCORE[LM];
SCORE *DPD_ = new SCORE[LM];
SCORE *DPI_ = new SCORE[LM];
char *TBM_ = new char[LM];
char *TBD_ = new char[LM];
char *TBI_ = new char[LM];
DPM(0, 0) = 0;
DPD(0, 0) = MINUS_INFINITY;
DPI(0, 0) = MINUS_INFINITY;
TBM(0, 0) = 'S';
TBD(0, 0) = '?';
TBI(0, 0) = '?';
DPM(1, 0) = MINUS_INFINITY;
DPD(1, 0) = GapScoreMD(PA[0], PPTerm);
DPI(1, 0) = MINUS_INFINITY;
TBM(1, 0) = '?';
TBD(1, 0) = 'S';
TBI(1, 0) = '?';
DPM(0, 1) = MINUS_INFINITY;
DPD(0, 1) = MINUS_INFINITY;
DPI(0, 1) = GapScoreMI(PPTerm, PB[0]);
TBM(0, 1) = '?';
TBD(0, 1) = '?';
TBI(0, 1) = 'S';
// Empty prefix of B is special case
for (unsigned uPrefixLengthA = 2; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
{
// M=LetterA+LetterB, impossible with empty prefix
DPM(uPrefixLengthA, 0) = MINUS_INFINITY;
TBM(uPrefixLengthA, 0) = '?';
// D=LetterA+GapB
DPD(uPrefixLengthA, 0) = DPD(uPrefixLengthA - 1, 0) +
GapScoreDD(PA[uPrefixLengthA - 1], PPTerm);
TBD(uPrefixLengthA, 0) = 'D';
// I=GapA+LetterB, impossible with empty prefix
DPI(uPrefixLengthA, 0) = MINUS_INFINITY;
TBI(uPrefixLengthA, 0) = '?';
}
// Empty prefix of A is special case
for (unsigned uPrefixLengthB = 2; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
{
// M=LetterA+LetterB, impossible with empty prefix
DPM(0, uPrefixLengthB) = MINUS_INFINITY;
TBM(0, uPrefixLengthB) = '?';
// D=LetterA+GapB, impossible with empty prefix
DPD(0, uPrefixLengthB) = MINUS_INFINITY;
TBD(0, uPrefixLengthB) = '?';
// I=GapA+LetterB
DPI(0, uPrefixLengthB) = DPI(0, uPrefixLengthB - 1) +
GapScoreII(PPTerm, PB[uPrefixLengthB - 1]);
TBI(0, uPrefixLengthB) = 'I';
}
// ============
// Main DP loop
// ============
for (unsigned uPrefixLengthB = 1; uPrefixLengthB < uPrefixCountB; ++uPrefixLengthB)
{
const ProfPos &PPB = PB[uPrefixLengthB - 1];
for (unsigned uPrefixLengthA = 1; uPrefixLengthA < uPrefixCountA; ++uPrefixLengthA)
{
const ProfPos &PPA = PA[uPrefixLengthA - 1];
{
// Match M=LetterA+LetterB
SCORE scoreLL = ScoreProfPosDimer(PPA, PPB);
SCORE scoreMM = DPM(uPrefixLengthA-1, uPrefixLengthB-1) + GapScoreMM(PPA, PPB);
SCORE scoreDM = DPD(uPrefixLengthA-1, uPrefixLengthB-1) + GapScoreDM(PPA, PPB);
SCORE scoreIM = DPI(uPrefixLengthA-1, uPrefixLengthB-1) + GapScoreIM(PPA, PPB);
SCORE scoreBest = scoreMM;
char c = 'M';
if (scoreDM > scoreBest)
{
scoreBest = scoreDM;
c = 'D';
}
if (scoreIM > scoreBest)
{
scoreBest = scoreIM;
c = 'I';
}
DPM(uPrefixLengthA, uPrefixLengthB) = scoreBest + scoreLL;
TBM(uPrefixLengthA, uPrefixLengthB) = c;
}
{
// Delete D=LetterA+GapB
SCORE scoreMD = DPM(uPrefixLengthA-1, uPrefixLengthB) + GapScoreMD(PPA, PPB);
SCORE scoreDD = DPD(uPrefixLengthA-1, uPrefixLengthB) + GapScoreDD(PPA, PPB);
SCORE scoreID = DPI(uPrefixLengthA-1, uPrefixLengthB) + GapScoreID(PPA, PPB);
SCORE scoreBest = scoreMD;
char c = 'M';
if (scoreDD > scoreBest)
{
scoreBest = scoreDD;
c = 'D';
}
if (scoreID > scoreBest)
{
scoreBest = scoreID;
c = 'I';
}
DPD(uPrefixLengthA, uPrefixLengthB) = scoreBest;
TBD(uPrefixLengthA, uPrefixLengthB) = c;
}
{
// Insert I=GapA+LetterB
SCORE scoreMI = DPM(uPrefixLengthA, uPrefixLengthB-1) + GapScoreMI(PPA, PPB);
SCORE scoreDI = DPD(uPrefixLengthA, uPrefixLengthB-1) + GapScoreDI(PPA, PPB);
SCORE scoreII = DPI(uPrefixLengthA, uPrefixLengthB-1) + GapScoreII(PPA, PPB);
SCORE scoreBest = scoreMI;
char c = 'M';
if (scoreDI > scoreBest)
{
scoreBest = scoreDI;
c = 'D';
}
if (scoreII > scoreBest)
{
scoreBest = scoreII;
c = 'I';
}
DPI(uPrefixLengthA, uPrefixLengthB) = scoreBest;
TBI(uPrefixLengthA, uPrefixLengthB) = c;
}
}
}
#if TRACE
Log("DPM:\n");
ListDP(DPM_, PA, PB, uPrefixCountA, uPrefixCountB);
Log("DPD:\n");
ListDP(DPD_, PA, PB, uPrefixCountA, uPrefixCountB);
Log("DPI:\n");
ListDP(DPI_, PA, PB, uPrefixCountA, uPrefixCountB);
Log("TBM:\n");
ListTB(TBM_, PA, PB, uPrefixCountA, uPrefixCountB);
Log("TBD:\n");
ListTB(TBD_, PA, PB, uPrefixCountA, uPrefixCountB);
Log("TBI:\n");
ListTB(TBI_, PA, PB, uPrefixCountA, uPrefixCountB);
#endif
SCORE Score = TraceBackDimer(DPM_, DPD_, DPI_, TBM_, TBD_, TBI_,
uLengthA, uLengthB, Path);
#if TRACE
Log("GlobalAlignDimer score = %.3g\n", Score);
#endif
delete[] DPM_;
delete[] DPD_;
delete[] DPI_;
delete[] TBM_;
delete[] TBD_;
delete[] TBI_;
return Score;
}
