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();
}
//__________________________________________________________________________________
long DisplayListOfChoices (void)
{
ReadInTemplateFiles();
if (!availableTemplateFiles.lLength)
return -1;
long choice = -1;
char buffer[2048];
_String fileAbbr,
*thisLine;
_SimpleList categoryDelimiters;
_List categoryHeadings;
for (choice = 0; choice< availableTemplateFiles.lLength; choice++)
{
thisLine = (_String*)(*(_List*)availableTemplateFiles(choice))(2);
if (thisLine->sData[0]=='!')
{
categoryDelimiters<<choice;
fileAbbr = *thisLine;
fileAbbr.Trim (1,-1);
categoryHeadings && &fileAbbr;
}
}
choice = -1;
if (categoryDelimiters.lLength==0)
{
while (choice == -1)
{
for (choice = 0; choice<availableTemplateFiles.lLength; choice++)
{
printf ("\n\t(%s):%s",((_String*)(*(_List*)availableTemplateFiles(choice))(0))->getStr(),
((_String*)(*(_List*)availableTemplateFiles(choice))(1))->getStr());
}
printf ("\n\n Please type in the abbreviation for the file you want to use (or press ENTER to process custom batch file):");
fgets (buffer,2048,stdin);
fgets (buffer,2048,stdin);
fileAbbr = buffer;
if (fileAbbr.FirstNonSpaceIndex()<0)
return -1;
fileAbbr.UpCase();
for (choice = 0; choice<availableTemplateFiles.lLength; choice++)
{
if (fileAbbr.Equal((_String*)(*(_List*)availableTemplateFiles(choice))(0)))
break;
}
if (choice==availableTemplateFiles.lLength) choice=-1;
}
}
else
{
long categNumber = -1;
while (choice==-1)
{
if (categNumber<0)
{
_String header ("***************** TYPES OF STANDARD ANALYSES *****************"),
verString (GetVersionString().getStr());
if (verString.sLength<header.sLength-2)
{
_String padder (128,true);
long poop = (header.sLength-2-verString.sLength)/2;
if (!poop) poop = 1;
for (choice=0; choice<poop; choice++)
padder << ' ';
padder.Finalize();
verString = padder & '/' & verString & "\\" & padder;
}
printf ("\n\033[2J\033[H%s\n%s\n\n",verString.getStr(), header.getStr());
for (choice = 0; choice<categoryHeadings.lLength; choice++)
printf ("\n\t(%ld) %s",choice+1,((_String*)categoryHeadings(choice))->getStr());
printf ("\n\n Please select type of analyses you want to list (or press ENTER to process custom batch file):");
fgets (buffer,2048,stdin);
fileAbbr = buffer;
if (logInputMode)
loggedUserInputs && & fileAbbr;
if (fileAbbr.FirstNonSpaceIndex()<0)
return -1;
choice = fileAbbr.toNum();
if ( choice>0 && choice<=categoryHeadings.lLength)
categNumber = choice-1;
}
else
{
printf ("\n\033[2J\033[H ***************** FILES IN '%s' ***************** \n\n",((_String*)categoryHeadings(categNumber))->getStr());
long start = categoryDelimiters.lData[categNumber]+1,
end = categNumber==categoryDelimiters.lLength-1?availableTemplateFiles.lLength:categoryDelimiters.lData[categNumber+1];
for (choice = start; choice<end; choice++)
printf ("\n\t(%ld) %s",choice-start+1,((_String*)(*(_List*)availableTemplateFiles(choice))(1))->getStr());
printf ("\n\n Please select the file you want to use (or press ENTER to return to the list of analysis types):");
fileAbbr = *StringFromConsole ();
if (logInputMode)
loggedUserInputs && & fileAbbr;
if (fileAbbr.FirstNonSpaceIndex()<0)
categNumber = -1;
else
{
choice = fileAbbr.toNum();
if ((choice>0 && choice<=end-start))
return start+choice-1;
}
}
choice = -1;
}
}
return choice;
}
int main( int argc, char *argv[] )
{
#ifdef __HYPHYMPI__
int rank,
size;
MPI_Init (&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
_hy_mpi_node_rank = rank;
setParameter (mpiNodeID, (_Parameter)rank);
setParameter (mpiNodeCount, (_Parameter)size);
if (rank == 0)
#endif
gtk_init (&argc, &argv);
/* set up globals */
char curWd[4096];
getcwd (curWd,4096);
_String baseDir (curWd);
baseDir=baseDir&'/';
pathNames&& &baseDir;
baseDirectory = baseDir;
for (long i=1; i<argc;i++)
{
_String thisArg (argv[i]);
if (thisArg.beginswith ("BASEPATH="))
{
baseDirectory = thisArg.Cut(9,-1);
if (baseDirectory.sLength)
{
if (baseDirectory.sData[baseDirectory.sLength-1]!='/')
baseDirectory = baseDirectory&"/";
}
}
else
if (thisArg.beginswith ("USEPATH="))
{
_String baseArgDir (thisArg,8,-1);
errorFileName = baseArgDir & errorFileName;
messageFileName = baseArgDir & messageFileName;
pathNames.Delete (0);
pathNames&& &baseDir;
}
else
if (thisArg.beginswith ("CPU="))
{
#ifdef __MP__
_String cpus = thisArg.Cut(4,-1);
systemCPUCount = cpus.toNum();
if (systemCPUCount<1)
systemCPUCount = 1;
#ifdef __MP2__
pthread_setconcurrency (systemCPUCount+1);
#endif
#endif
}
#ifdef __HYPHYMPI__
else
if (thisArg == _String("MPIOPTIMIZER"))
{
mpiParallelOptimizer = true;
setParameter (mpiNodeCount, 0.0);
}
else
if (thisArg == _String("MPIPARTITIONS"))
{
mpiPartitionOptimizer = true;
setParameter (mpiNodeCount, 0.0);
}
#endif
}
#ifdef __HYPHYMPI__
if (rank == 0)
#endif
{
baseDir = baseDirectory & "GTKResources";
_List scanRes;
ScanDirectoryForFileNames(baseDir,scanRes,false);
if (scanRes.lLength == 0)
{
GtkWidget * noRez = gtk_message_dialog_new (NULL, GTK_DIALOG_MODAL, GTK_MESSAGE_ERROR, GTK_BUTTONS_OK, "HYPHY_GTK was unable to find a required GTKResources directory in %s. Please use BASEPATH= command line option to specify where the installation directory of HyPhy can be found.", baseDirectory.sData);
gtk_dialog_run (GTK_DIALOG (noRez));
gtk_widget_destroy (noRez);
return 1;
}
_String rcPath = baseDir & "/theme/theme.rc";
//printf ("Loading res files from %s\n", rcPath.sData);
gtk_rc_parse (rcPath.sData);
}
GlobalStartup();
#ifdef __HYPHYMPI__
if (rank == 0)
{
#endif
GdkDisplay * defDisplay = gdk_screen_get_display (gdk_screen_get_default());
hSizeCursor = gdk_cursor_new_for_display (defDisplay,GDK_SB_H_DOUBLE_ARROW);
pickUpCursor = gdk_cursor_new_for_display (defDisplay,GDK_TARGET);
dropOffCursor = gdk_cursor_new_for_display (defDisplay,GDK_TCROSS);
screenPContext = gdk_pango_context_get_for_screen (gdk_screen_get_default());
tablePDMenuIcon = (GdkPixbuf*)ProcureIconResource(4020);
/*{
GdkScreen * defD = gdk_screen_get_default();
fontConversionFactor = 72.27 / (gdk_screen_get_height (defD) *25.4 / gdk_screen_get_height_mm(defD));
printf ("Pango conversion factor computed at: %g\n", fontConversionFactor);
}*/
ReadInTemplateFiles ();
hyphyConsoleWindow = new _HYConsoleWindow ("HYPHY Console");
ReadPreferences ();
SetStatusLine ("None","Idle","00:00:00");
while (gtk_events_pending())
gtk_main_iteration();
SetPreferences ();
ReadGeneticCodes ();
ReadModelTemplates ();
ReadTreeProcessors ();
MoveConsoleWindow (consolePositionRectangle);
StringToConsole (hyphyCiteString);
hyphyConsoleWindow->BringToFront();
#ifdef __HYPHYMPI__
{
char statBuffer[1024];
sprintf (statBuffer,"MPI version of HyPhy running on %d nodes (a master and %d compute nodes) in %s mode\n",
size,
size-1,
mpiPartitionOptimizer?"partition":(mpiParallelOptimizer?"rate heterogeneity":"normal"));
BufferToConsole (statBuffer);
}
#endif
g_timeout_add (100,GlobalQueueTimer,nil);
g_timeout_add (1000,progressTimerFunction,nil);
gtk_main ();
WritePreferences();
#ifdef __HYPHYMPI__
}
else // slave node
{
if (mpiParallelOptimizer || mpiPartitionOptimizer)
mpiOptimizerLoop (rank, size);
else
mpiNormalLoop (rank, size, baseDir);
}
#endif
GlobalShutdown();
return 0;
}