Window FindWindow(char* szWindowToFind)
{
Display *display = XOpenDisplay (NULL);
int screen = DefaultScreen (display);
XSetErrorHandler(ErrorHandler);
Window rootWindow = RootWindow (display, screen);
Window wSearchedWindow = SearchWindow(szWindowToFind, 0, display,
rootWindow, 0, 0);
char* win_name;
if (XFetchName(display, wSearchedWindow, &win_name))
{
printf("Found: %s\n", win_name);
}
XCloseDisplay (display);
return wSearchedWindow;
}
BOOL CALLBACK SearchWindowDialogProc
(
HWND hwndDlg, // handle to dialog box
UINT uMsg, // message
WPARAM wParam, // first message parameter
LPARAM lParam // second message parameter
)
{
BOOL bRet = FALSE; // Default return value.
switch (uMsg)
{
case WM_INITDIALOG:
{
if (isParentKill) CheckDlgButton(hwndDlg, IDC_CHECK1, 1);
bRet = TRUE;
break;
}
case WM_MOUSEMOVE:
{
bRet = TRUE;
if (g_bStartSearchWindow)
{
// Only when we have started the Window Searching operation will we
// track mouse movement.
DoMouseMove(hwndDlg, uMsg, wParam, lParam);
}
break;
}
case WM_LBUTTONUP:
{
bRet = TRUE;
if (g_bStartSearchWindow)
{
// Only when we have started the window searching operation will we
// be interested when the user lifts up the left mouse button.
DoMouseUp(hwndDlg, uMsg, wParam, lParam);
}
break;
}
case WM_COMMAND:
{
WORD wNotifyCode = HIWORD(wParam); // notification code
WORD wID = LOWORD(wParam); // item, control, or accelerator identifier
HWND hwndCtl = (HWND)lParam; // handle of control
if ((wID == IDOK))
{
if (hStoreWnd != hwndDlg)
{
HWND hTargetWnd = hStoreWnd;
if (IsDlgButtonChecked(hwndDlg, IDC_CHECK1))
{
while (GetParent(hTargetWnd))
{
hTargetWnd = GetParent(hTargetWnd);
}
isParentKill = true;
}
else
isParentKill = false;
SetParent(hTargetWnd, hwndDlg);
}
bRet = TRUE;
EndDialog(hwndDlg, wID);
}
else if (wID == IDCANCEL)
{
ExitProcess(0);
}
if (wID == IDC_STATIC_ICON_FINDER_TOOL)
{
// Because the IDC_STATIC_ICON_FINDER_TOOL static control is set with the SS_NOTIFY
// flag, the Search Window's dialog box will be sent a WM_COMMAND message when this
// static control is clicked.
bRet = TRUE;
// We start the window search operation by calling the DoSearchWindow() function.
SearchWindow(hwndDlg);
break;
}
break;
}
default:
{
bRet = FALSE;
break;
}
}
return bRet;
}
short AssembleOneSV(std::map<std::string,int> &ChrName2Index, ControlState & CurrentState, const Assembly & OneSV, std::ofstream & ASM_Output) {
//std::cout << "AssembleOneSV 1" << std::endl;
//short Max_NT_Size = 30;
bool WhetherFirstBP = true;
std::vector <SPLIT_READ> First, Second;
unsigned SearchCenter;
unsigned SearchRange;
std::cout << "Current SV: " << OneSV.Index << " " << OneSV.Type << " " << OneSV.ChrA << " " << OneSV.PosA << " " << OneSV.CI_A
<< "\t" << OneSV.ChrB << " " << OneSV.PosB << " " << OneSV.CI_B << std::endl;
// get first BP
CurrentState.Reads_SR.clear();
CurrentState.OneEndMappedReads.clear();
//std::cout << "AssembleOneSV 2" << std::endl;
const Chromosome* currentChromosomeFirst = g_genome.getChr(OneSV.ChrA);
const Chromosome* currentChromosomeSecond = g_genome.getChr(OneSV.ChrB);
std::string FirstChrSeq = currentChromosomeFirst->getSeq();
std::string SecondChrSeq = currentChromosomeSecond->getSeq();
if (CurrentState.CurrentChrName != OneSV.ChrA) {
CurrentState.CurrentChrName = OneSV.ChrA;
CurrentState.CurrentChrSeq = FirstChrSeq;
//CurrentState.CurrentChrSeq = AllChromosomes[ChrName2Index.find(OneSV.ChrA)->second].ChrSeq; // change later, copying one chrseq for each SV is expensive.
}
//const unsigned CONS_Chr_Size = currentChromosome->getBiolSize(); // #################
//std::cout << "CONS_Chr_Size " << CONS_Chr_Size << std::endl;
g_maxPos = 0; // #################
unsigned Left, Right;
unsigned int lowerBinBorder = 1;
if (OneSV.PosA > OneSV.CI_A + 1000)
lowerBinBorder = OneSV.PosA - OneSV.CI_A - 1000; //CurrentState.
unsigned int upperBinBorder = OneSV.PosA + OneSV.CI_A + 1000;
SearchWindow window( currentChromosomeFirst, lowerBinBorder, upperBinBorder );
Left = OneSV.PosA + g_SpacerBeforeAfter - OneSV.CI_A;
Right = OneSV.PosA + g_SpacerBeforeAfter + OneSV.CI_A;
std::cout << "\nFirst BP\tChrName " << CurrentState.CurrentChrName << "\tRange " << lowerBinBorder << " " << upperBinBorder << std::endl;
get_SR_Reads(CurrentState, window );
//std::cout << "First size: " << CurrentState.Reads_SR.size() << std::endl;
CombineAndSort(ChrName2Index, CurrentState, OneSV, First, lowerBinBorder, upperBinBorder, WhetherFirstBP);
CleanUpCloseEnd(First, Left, Right); // vector of reads
std::cout << "\nFirst size " << First.size() << std::endl;
SearchRange = OneSV.CI_B + 1000;
SearchCenter = OneSV.PosB + g_SpacerBeforeAfter;
std::vector< SearchWindow > searchCluster;
searchCluster.push_back( SearchWindow( currentChromosomeSecond, SearchCenter-SearchRange, SearchCenter+SearchRange ) );
Left = OneSV.PosB + g_SpacerBeforeAfter - OneSV.CI_B;
Right = OneSV.PosB + g_SpacerBeforeAfter + OneSV.CI_B;
for (unsigned ReadIndex = 0; ReadIndex < First.size(); ReadIndex++) {
First[ReadIndex].FarFragName = OneSV.ChrB;
//SearchFarEndAtPos(AllChromosomes[ChrName2Index.find(OneSV.ChrB)->second].ChrSeq, First[ReadIndex], SearchCenter, SearchRange);
SearchFarEndAtPos(SecondChrSeq, First[ReadIndex], searchCluster);
}
//std::cout << "AssembleOneSV 7" << std::endl;
CleanUpFarEnd(First, Left, Right);
//std::cout << "AssembleOneSV 8" << std::endl;
for (unsigned ReadIndex = 0; ReadIndex < First.size(); ReadIndex++) {
if (First[ReadIndex].UP_Close.size()) {
if (First[ReadIndex].UP_Far.size()) {
OutputCurrentRead(ChrName2Index, CurrentState, OneSV, First[ReadIndex], ASM_Output);
}
}
}
// get second BP
CurrentState.Reads_SR.clear();
WhetherFirstBP = false;
CurrentState.CurrentChrName = OneSV.ChrB;
CurrentState.CurrentChrSeq = SecondChrSeq;
//CONS_Chr_Size = CurrentState.CurrentChrSeq.size() - 2 * g_SpacerBeforeAfter; // #################
g_maxPos = 0; // #################
lowerBinBorder = 1;
if (OneSV.PosB > OneSV.CI_B + 1000)
lowerBinBorder = OneSV.PosB - OneSV.CI_B - 1000;
upperBinBorder = OneSV.PosB + OneSV.CI_B + 1000;
SearchWindow window2( currentChromosomeSecond, lowerBinBorder, upperBinBorder );
Left = OneSV.PosB + g_SpacerBeforeAfter - OneSV.CI_B;
Right = OneSV.PosB + g_SpacerBeforeAfter + OneSV.CI_B;
std::cout << "\nSecond BP\tChrName " << CurrentState.CurrentChrName << "\tRange " << lowerBinBorder << " " << upperBinBorder << std::endl;
get_SR_Reads(CurrentState, window2 );
CombineAndSort(ChrName2Index, CurrentState, OneSV, Second, lowerBinBorder, upperBinBorder, WhetherFirstBP);
CleanUpCloseEnd(Second, Left, Right);
std::cout << "\nSecond size " << Second.size() << std::endl;
SearchRange = OneSV.CI_A + 1000;
SearchCenter = OneSV.PosA + g_SpacerBeforeAfter;
Left = OneSV.PosA + g_SpacerBeforeAfter - OneSV.CI_A;
Right = OneSV.PosA + g_SpacerBeforeAfter + OneSV.CI_A;
searchCluster.clear();
searchCluster.push_back( SearchWindow( currentChromosomeFirst, SearchCenter-SearchRange, SearchCenter+SearchRange ) );
for (unsigned ReadIndex = 0; ReadIndex < Second.size(); ReadIndex++) {
Second[ReadIndex].FarFragName = OneSV.ChrA;
//SearchFarEndAtPos(AllChromosomes[ChrName2Index.find(OneSV.ChrA)->second].ChrSeq, Second[ReadIndex], SearchCenter, SearchRange);
SearchFarEndAtPos(FirstChrSeq, Second[ReadIndex], searchCluster);
}
CleanUpFarEnd(Second, Left, Right);
for (unsigned ReadIndex = 0; ReadIndex < Second.size(); ReadIndex++) {
if (Second[ReadIndex].UP_Close.size()) {
if (Second[ReadIndex].UP_Far.size()) {
OutputCurrentRead(ChrName2Index, CurrentState, OneSV, Second[ReadIndex], ASM_Output);
}
}
}
unsigned SumSize = 0;
for (unsigned ReadIndex = 0; ReadIndex < First.size(); ReadIndex++) {
SumSize += First[ReadIndex].UP_Far.size();
}
for (unsigned ReadIndex = 0; ReadIndex < Second.size(); ReadIndex++) {
SumSize += Second[ReadIndex].UP_Far.size();
}
if (SumSize == 0 && OneSV.ChrA == OneSV.ChrB) {
TryLI(ChrName2Index, CurrentState, OneSV, First, Second, ASM_Output);
}
return 0;
}
// Recursively search through all windows on display
Window SearchWindow(char* szWindowToFind, int level, Display *display,
Window rootWindow, int iMatchMode, int showErrors)
{
Window parent;
Window *children;
unsigned int noOfChildren;
int status;
unsigned int i;
Window wSearchedWindow = 0;
char* win_name;
if (XFetchName(display, rootWindow, &win_name))
{
//printf("WinName (Level %d): %s\n", level, win_name);
if(iMatchMode == 0)
{
if( strstr(win_name, szWindowToFind) )
{
return rootWindow;
}
}
else if(iMatchMode == 1)
{
if( !strcmp(win_name, szWindowToFind) )
{
return rootWindow;
}
}
else if(iMatchMode == 2)
{
if( strcasestr(win_name, szWindowToFind) )
{
return rootWindow;
}
}
else if(iMatchMode == 3)
{
if( !strcasecmp(win_name, szWindowToFind) )
{
return rootWindow;
}
}
else
{
if( strstr(win_name, szWindowToFind) )
{
return rootWindow;
}
}
} // End if XFetchName
status = XQueryTree (display, rootWindow, &rootWindow,
&parent, &children, &noOfChildren);
if (status == 0)
{
if (showErrors)
printf ("ERROR - Could not query the window tree. Aborting.\r\n");
return rootWindow;
}
if (noOfChildren > 0)
{
for (i=0; i < noOfChildren; i++)
{
wSearchedWindow = SearchWindow(szWindowToFind, level+1, display, children[i], iMatchMode, showErrors);
if(wSearchedWindow)
{
break;
}
}
}
XFree ((char*) children);
return wSearchedWindow;
} // End Sub EnumerateWindows