_String _HYStandardDirectory (const unsigned long which_one) {
_String dirSpacer (GetPlatformDirectoryChar());
switch (which_one) {
case HY_HBL_DIRECTORY_TEMPLATE_MODELS:
return libDirectory & "TemplateBatchFiles" & dirSpacer & "TemplateModels" & dirSpacer;
}
return empty;
}
int main(int argc, char *argv[])
{
GlobalStartup();
DoApplicationSettings ();
char curWd[4096],
dirSlash = GetPlatformDirectoryChar ();
getcwd (curWd,4096);
_String baseDir (curWd);
if (baseDir.getChar (baseDir.sLength-1) != dirSlash) {
baseDir=baseDir & dirSlash;
}
_String libDir (_HYPHY_LIBDIRECTORY_);
if (libDir.getChar (libDir.sLength-1) != dirSlash) {
libDir=libDir & dirSlash;
}
pathNames&& &libDir;
libDirectory = libDir;
libArgDir = libDirectory;
baseDirectory = baseDir;
baseArgDir = baseDirectory;
QApplication app(argc, argv);
HyphyMain mainWindow;
ReadInTemplateFiles ();
_hyPrimaryConsoleWindow = & mainWindow;
/*mainWindow.setGeometry(
QStyle::alignedRect(
Qt::LeftToRight,
Qt::AlignCenter,
mainWindow.size(),
qApp->desktop()->availableGeometry()
));*/
mainWindow.show();
mainWindow.raise();
return app.exec();
}
bool PushFilePath (_String& pName, bool trim)
{
char c = GetPlatformDirectoryChar();
long f = pName.FindBackwards(_String(c),0,-1);
if (f>=0) {
_String newP = pName.Cut(0,f);
pathNames && & newP;
if (trim)
pName.Trim (f+1,-1);
return true;
} else if (pathNames.lLength) {
pathNames && pathNames(pathNames.lLength-1);
} else {
pathNames && & empty;
}
return false;
}
void _THyPhy::InitTHyPhy (_ProgressCancelHandler* mHandler, const char* baseDirPath, long cpuCount)
{
char dirSlash = GetPlatformDirectoryChar ();
systemCPUCount = cpuCount;
SetCallbackHandler (mHandler);
checkPointer (currentResultHolder = new _THyPhyString);
askFID = -1;
if (baseDirPath)
// set base directory
{
baseDirectory = baseDirPath;
if (baseDirectory.getChar(baseDirectory.sLength-1) != dirSlash) {
baseDirectory = baseDirectory & dirSlash;
}
baseDirectoryInstance = new _THyPhyString (baseDirectory.sData);
baseDirectory = baseDirectoryInstance->sData;
pathNames && &baseDirectory;
ReadPreferences ();
}
#ifdef _HYPHY_LIBDIRECTORY_
libDirectory = _HYPHY_LIBDIRECTORY_;
if (libDirectory.getChar(libDirectory.sLength-1) != dirSlash) {
libDirectory = libDirectory & dirSlash;
}
pathNames && &libDirectory;
#else
if (baseDirectory)
libDirectory = baseDirectory;
#endif
GlobalStartup();
errors = nil;
warnings = nil;
textout = nil;
globalInterfaceInstance = this;
}
//__________________________________________________________________________________
int main (int argc, char* argv[])
{
mainArgCount = argc - 1;
#ifdef __HYPHYMPI__
int rank,
size;
MPI_Init (&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
setParameter (mpiNodeID, (_Parameter)rank);
setParameter (mpiNodeCount, (_Parameter)size);
_hy_mpi_node_rank = rank;
if (rank == 0)
{
mpiNodesThatCantSwitch.Populate (size,1,0);
/* {
char hostname[256];
gethostname(hostname, sizeof(hostname));
printf("PID %d on %s ready for attach\n", getpid(), hostname);
fflush(stdout);
//getchar ();
} */
#endif
//for (long k=0; k<NSIG; k++)
//{
// signal(k, &hyphyBreak);
//}
#ifdef __HYPHYMPI__
}
#endif
char curWd[4096],
dirSlash = GetPlatformDirectoryChar ();
getcwd (curWd,4096);
_String baseDir (curWd),
argFile;
baseDir=baseDir & dirSlash;
pathNames&& &baseDir;
baseDirectory = baseDir;
baseArgDir = baseDirectory;
_ExecutionList ex;
#ifdef _OPENMP
systemCPUCount = omp_get_max_threads();
#endif
#ifdef _MINGW32_MEGA_
{
char pid[16];
snprintf (pid,16,"%u", GetCurrentProcessId());
_String pipeName = _String("\\\\.\\pipe\\MEGAPipe") & pid;
printf ("Pipe name = %s\n", pipeName.sData);
if ((_HY_MEGA_Pipe = CreateFile(pipeName.sData, GENERIC_WRITE, 0, NULL, OPEN_EXISTING, 0, NULL)) == INVALID_HANDLE_VALUE)
{
char* lpMsgBuf;
FormatMessage(
FORMAT_MESSAGE_ALLOCATE_BUFFER |
FORMAT_MESSAGE_FROM_SYSTEM |
FORMAT_MESSAGE_IGNORE_INSERTS,
NULL,
GetLastError(),
MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT),
(LPTSTR) &lpMsgBuf,
0, NULL );
FlagError (_String("Failed to create a pipe named '") & pipeName & "' to send data from HyPhy to MEGA. Error: "&lpMsgBuf);
}
}
#endif
for (long i=1; i<argc;i++)
{
_String thisArg (argv[i]);
if (thisArg.sData[0]=='-')
{
ProcessConfigStr (thisArg);
}
else
if (thisArg.beginswith ("BASEPATH="))
{
baseArgDir = thisArg.Cut(9,-1);
if (baseArgDir.sLength)
{
if (baseArgDir.sData[baseArgDir.sLength-1]!=dirSlash)
baseArgDir = baseArgDir&dirSlash;
baseDirectory = baseArgDir;
}
}
else
if (thisArg.beginswith ("USEPATH="))
{
baseDir = thisArg.Cut(8,-1);
errorFileName = baseDir & errorFileName;
messageFileName = baseDir & messageFileName;
pathNames.Delete (0);
pathNames&& &baseDir;
}
else
#ifdef __MP__
if (thisArg.beginswith ("CPU="))
{
_String cpus = thisArg.Cut(4,-1);
systemCPUCount = cpus.toNum();
if (systemCPUCount<1)
systemCPUCount = 1;
pthread_setconcurrency (systemCPUCount+1);
}
else
#endif
argFile = thisArg;
}
GlobalStartup();
if (calculatorMode)
{
printf ("\nHYPHY is running in calculator mode. Type 'exit' when you are finished.\n");
while (ExpressionCalculator()) ;
return 0;
}
if (pipeMode)
{
_String bfIn (stdin);
_ExecutionList exIn (bfIn);
exIn.Execute();
GlobalShutdown();
return 0;
}
// try to read the preferences
_String prefFile (curWd);
prefFile = prefFile & '/' & prefFileName;
FILE * testPrefFile = fopen (prefFile.sData,"r");
if (!testPrefFile)
{
prefFile = baseArgDir & prefFileName;
testPrefFile = fopen (prefFile.sData,"r");
}
if (testPrefFile)
{
fclose(testPrefFile);
ReadBatchFile (prefFile,ex);
ex.Execute();
ex.Clear();
}
//printf ("Node %d before mpiParallelOptimizer\n", rank);
#ifdef __HYPHYMPI__
if (rank>0)
{
//if (mpiParallelOptimizer || mpiPartitionOptimizer)
// mpiOptimizerLoop (rank, size);
//else
mpiNormalLoop (rank, size, baseDir);
/*argFile = "SHUTDOWN_CONFIRM";
MPISendString (argFile, senderID);*/
}
else
{
#endif
if (!argFile.sLength)
{
long selection = -2;
if (!updateMode)
selection = DisplayListOfChoices();
if (selection == -1)
{
dialogPrompt = "Batch file to run:";
_String fStr (ReturnDialogInput (true));
if (logInputMode)
{
_String tts = loggedFileEntry&fStr;
loggedUserInputs && & tts;
}
PushFilePath (fStr);
ReadBatchFile (fStr,ex);
}
else
{
_String templ;
if (selection >= 0)
templ = baseArgDir &"TemplateBatchFiles" & dirSlash;
else
templ = baseArgDir & "TemplateBatchFiles" & dirSlash & "WebUpdate.bf";
if (selection >= 0)
templ= templ&*(_String*)(*(_List*)availableTemplateFiles(selection))(2);
PushFilePath (templ);
ReadBatchFile (templ,ex);
}
}
else
{
#ifndef __MINGW32__
if (argFile.sData[0] != '/')
argFile = baseDirectory & argFile;
#else
if (argFile.sData[1] != ':') // not an absolute path
argFile = baseDirectory & argFile;
#endif
PushFilePath (argFile);
ReadBatchFile (argFile,ex);
}
ex.Execute();
if (usePostProcessors && (!updateMode))
{
ReadInPostFiles();
printf ("\n\n**********Continue with result processing (y/n)?");
_String c_str (StringFromConsole());
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.getChar(0) !='n' && c_str.getChar(0)!='N' )
{
long choice = DisplayListOfPostChoices();
while (choice != -1)
{
_ExecutionList postEx;
argFile = *(_String*)(*(_List*)availablePostProcessors(choice-1))(1);
PushFilePath (argFile);
ReadBatchFile (argFile, postEx);
postEx.Execute();
PopFilePath ();
printf ("\n\n**********Continue with result processing (y/n)?");
c_str = StringFromConsole();
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.getChar(0)=='n' || c_str.getChar(0)=='N' )
break;
choice = DisplayListOfPostChoices();
}
}
}
#ifdef __HYPHYMPI__
}
ReportWarning (_String ("Node ") & (long)rank & " is shutting down\n");
#endif
#ifdef _MINGW32_MEGA_
if (_HY_MEGA_Pipe != INVALID_HANDLE_VALUE)
CloseHandle (_HY_MEGA_Pipe);
#endif
PurgeAll (true);
GlobalShutdown ();
#ifdef __HYPHYMPI__
if (rank == 0)
printf ("\n\n");
#endif
}
//__________________________________________________________________________________
int main (int argc, char* argv[])
{
mainArgCount = argc - 1;
#ifdef __HYPHYMPI__
int rank,
size;
MPI_Init (&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
setParameter (mpiNodeID, (_Parameter)rank);
setParameter (mpiNodeCount, (_Parameter)size);
_hy_mpi_node_rank = rank;
if (rank == 0)
{
#endif
//for (long k=0; k<NSIG; k++)
//{
// signal(k, &hyphyBreak);
//}
#ifdef __HYPHYMPI__
}
#endif
char curWd[4096],
dirSlash = GetPlatformDirectoryChar ();
getcwd (curWd,4096);
_String baseDir (curWd),
argFile;
baseDir=baseDir & dirSlash;
pathNames&& &baseDir;
baseDirectory = baseDir;
baseArgDir = baseDirectory;
_ExecutionList ex;
#ifdef _OPENMP
systemCPUCount = omp_get_max_threads();
#endif
for (long i=1; i<argc;i++)
{
_String thisArg (argv[i]);
if (thisArg.sData[0]=='-')
{
ProcessConfigStr (thisArg);
}
else
if (thisArg.beginswith ("BASEPATH="))
{
baseArgDir = thisArg.Cut(9,-1);
if (baseArgDir.sLength)
{
if (baseArgDir.sData[baseArgDir.sLength-1]!=dirSlash)
baseArgDir = baseArgDir&dirSlash;
baseDirectory = baseArgDir;
}
}
else
if (thisArg.beginswith ("USEPATH="))
{
baseDir = thisArg.Cut(8,-1);
errorFileName = baseDir & errorFileName;
messageFileName = baseDir & messageFileName;
pathNames.Delete (0);
pathNames&& &baseDir;
}
else
#ifdef __MP__
if (thisArg.beginswith ("CPU="))
{
_String cpus = thisArg.Cut(4,-1);
systemCPUCount = cpus.toNum();
if (systemCPUCount<1)
systemCPUCount = 1;
#ifdef __MP2__
pthread_setconcurrency (systemCPUCount+1);
#endif
}
else
#endif
#ifdef __HYPHYMPI__
if (thisArg == _String("MPIOPTIMIZER"))
{
mpiParallelOptimizer = true;
setParameter (mpiNodeCount, 0.0);
}
else
if (thisArg == _String("MPIPARTITIONS"))
{
mpiPartitionOptimizer = true;
setParameter (mpiNodeCount, 0.0);
}
else
#endif
argFile = thisArg;
}
GlobalStartup();
if (calculatorMode)
{
printf ("\nHYPHY is running in calculator mode. Type 'exit' when you are finished.\n");
while (ExpressionCalculator()) ;
return 0;
}
if (pipeMode)
{
_String bfIn (stdin);
_ExecutionList exIn (bfIn);
exIn.Execute();
GlobalShutdown();
return 0;
}
// try to read the preferences
_String prefFile (curWd);
prefFile = prefFile & '/' & prefFileName;
FILE * testPrefFile = fopen (prefFile.sData,"r");
if (!testPrefFile)
{
prefFile = baseArgDir & prefFileName;
testPrefFile = fopen (prefFile.sData,"r");
}
if (testPrefFile)
{
fclose(testPrefFile);
ReadBatchFile (prefFile,ex);
ex.Execute();
ex.Clear();
}
//printf ("Node %d before mpiParallelOptimizer\n", rank);
#ifdef __HYPHYMPI__
if (rank>0)
{
if (mpiParallelOptimizer || mpiPartitionOptimizer)
mpiOptimizerLoop (rank, size);
else
mpiNormalLoop (rank, size, baseDir);
/*argFile = "SHUTDOWN_CONFIRM";
MPISendString (argFile, senderID);*/
}
else
{
#endif
if (!argFile.sLength)
{
long selection = -2;
if (!updateMode)
selection = DisplayListOfChoices();
if (selection == -1)
{
dialogPrompt = "Batch file to run:";
_String fStr (ReturnDialogInput (true));
if (logInputMode)
{
_String tts = loggedFileEntry&fStr;
loggedUserInputs && & tts;
}
PushFilePath (fStr);
ReadBatchFile (fStr,ex);
}
else
{
_String templ;
if (selection >= 0)
templ = baseArgDir &"TemplateBatchFiles" & dirSlash;
else
templ = baseArgDir & "TemplateBatchFiles" & dirSlash & "WebUpdate.bf";
if (selection >= 0)
templ= templ&*(_String*)(*(_List*)availableTemplateFiles(selection))(2);
PushFilePath (templ);
ReadBatchFile (templ,ex);
}
}
else
{
#ifndef __MINGW32__
if (argFile.sData[0] != '/')
argFile = baseDirectory & argFile;
#else
if (argFile.sData[1] != ':') // not an absolute path
argFile = baseDirectory & argFile;
#endif
PushFilePath (argFile);
ReadBatchFile (argFile,ex);
}
ex.Execute();
if (usePostProcessors && (!updateMode))
{
ReadInPostFiles();
printf ("\n\n**********Continue with result processing (y/n)?");
_String c_str (StringFromConsole());
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.sData[0]!='n' && c_str.sData[0]!='N' )
{
long choice = DisplayListOfPostChoices();
while (choice != -1)
{
_ExecutionList postEx;
argFile = *(_String*)(*(_List*)availablePostProcessors(choice-1))(1);
PushFilePath (argFile);
ReadBatchFile (argFile, postEx);
postEx.Execute();
PopFilePath ();
printf ("\n\n**********Continue with result processing (y/n)?");
_String c_str (StringFromConsole());
if (logInputMode)
loggedUserInputs && & c_str;
if (c_str.sData[0]=='n' || c_str.sData[0]=='N' ) break;
choice = DisplayListOfPostChoices();
}
}
}
#ifdef __HYPHYMPI__
}
argFile = _String ("Node ") & (long)rank & " is shutting down\n";
ReportWarning (argFile);
#endif
batchLanguageFunctions.Clear();
GlobalShutdown();
#ifdef __HYPHYMPI__
if (rank == 0)
printf ("\n\n");
#endif
}
