//__________________________________________________________________
void _HYSequencePane::CleanUpSequenceNames (void)
{
bool doSomething = false;
_List namesl;
_AVLList names (&namesl);
for (long k=0; k<speciesIndex.lLength; k++)
{
_String * thisString = (_String*)rowHeaders (speciesIndex.lData[k]);
if (!thisString->IsValidIdentifier(false))
{
BufferToConsole ("Changed ");
StringToConsole(*thisString);
thisString->ConvertToAnIdent(false);
BufferToConsole (" to ");
StringToConsole(*thisString);
NLToConsole();
doSomething = true;
}
_String * testString = new _String (*thisString);
if (!testString)
checkPointer (testString);
long tryThisSuffix = 2;
while (names.Find (testString)>=0)
{
*testString = *thisString & '_' & tryThisSuffix;
tryThisSuffix++;
}
if (tryThisSuffix>2)
{
BufferToConsole ("Changed ");
StringToConsole(*thisString);
BufferToConsole (" to ");
StringToConsole(*testString);
BufferToConsole (" to avoid duplicate identifiers\n");
doSomething = true;
thisString->CopyDynamicString (testString,true);
}
else
DeleteObject (testString);
names.Insert(thisString);
thisString->nInstances++;
}
if (doSomething)
{
SetHeaders (nil,true);
_MarkForUpdate();
}
}
//__________________________________________________________________________________
void SetStatusLineUser (_String s)
{
setvbuf(stdout, NULL, _IONBF, 0);
BufferToConsole("\33[2K\r");
StringToConsole(s);
needExtraNL = true;
}
//__________________________________________________________________________________
void SetStatusLine (_String s)
{
#ifdef _MINGW32_MEGA_
if (_HY_MEGA_Pipe != INVALID_HANDLE_VALUE) {
DWORD bytesWritten = 0;
if (WriteFile (_HY_MEGA_Pipe,(LPCVOID)s.sData,s.sLength,&bytesWritten,NULL) == FALSE || bytesWritten != s.sLength) {
_String errMsg ("Failed to write the entire status update to a named MEGA pipe");
StringToConsole (errMsg);
}
FlushFileBuffers(_HY_MEGA_Pipe);
} else {
StringToConsole (s);
}
#endif
}
bool ExpressionCalculator (void)
{
_String data (StringFromConsole(false));
#ifndef __UNIX__
if (terminateExecution) {
return false;
}
BufferToConsole (">");
StringToConsole (data);
BufferToConsole ("\n");
#endif
if (data.sLength == 4) {
_String checkForExit (data);
checkForExit.LoCase();
if (checkForExit == _String ("exit")) {
return false;
}
}
_Formula lhs,
rhs;
_FormulaParsingContext fpc;
long retCode = Parse(&lhs, data, fpc, nil);
if (!terminateExecution) {
if (retCode == HY_FORMULA_EXPRESSION) {
_PMathObj formRes = lhs.Compute();
if (!formRes) {
BufferToConsole ("NULL\n");
} else {
_String * objValue = (_String*)formRes->toStr();
StringToConsole (*objValue);
//BufferToConsole ("\n");
DeleteObject (objValue);
}
} else {
BufferToConsole ("NO RETURN VALUE");
}
}
NLToConsole();
terminateExecution = false;
return true;
}
_String ReturnDialogInput(bool dispPath)
{
if (!dispPath) {
NLToConsole ();
StringToConsole (dialogPrompt);
BufferToConsole (":");
} else {
NLToConsole ();
if (pathNames.lLength) {
StringToConsole(*(_String*)pathNames(pathNames.lLength-1));
} else {
StringToConsole (baseDirectory);
}
StringToConsole (dialogPrompt);
BufferToConsole (":");
}
return StringFromConsole();
}
bool ExpressionCalculator (_String data)
{
//Checking for exit
#ifndef __HYPHYQT__
if (data.sLength == 4) {
_String checkForExit (data);
checkForExit.LoCase();
if (checkForExit == _String ("exit")) {
return false;
}
}
#endif
_Formula lhs,
rhs;
_String errMsg;
_FormulaParsingContext fpc (&errMsg, nil);
long retCode = Parse(&lhs, data, fpc, nil);
if (retCode != HY_FORMULA_FAILED) {
if (retCode == HY_FORMULA_EXPRESSION) {
_PMathObj formRes = lhs.Compute(0,nil,nil,&errMsg);
if (errMsg.sLength) {
WarnError(errMsg);
} else {
_String * objValue = (_String*)formRes->toStr();
StringToConsole(*objValue);
DeleteObject(objValue);
}
} else {
BufferToConsole ("NO RETURN VALUE");
}
} else {
WarnError(errMsg);
}
return true;
}
void NLToConsole (void)
{
StringToConsole (newLN);
}
void BufferToConsole (const char* buffer)
{
_String s (buffer);
StringToConsole (s);
}
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;
}
