void _HYObjectInspector::OpenObject (void)
{
_HYPullDown* p1 = (_HYPullDown*)GetCellObject (0,2);
switch (p1->GetSelection()) {
case 0: {
OpenTreeFile();
break;
}
case 1: {
OpenDataFile();
break;
}
case 2: {
OpenModelFile();
break;
}
default:
return;
}
BuildListOfObjects (p1->GetSelection());
}
bool _HYConsoleWindow::_ProcessMenuSelection (long msel)
{
switch (msel) {
case HY_WINDOW_MENU_ID_FILE+1:
SaveConsole ();
return true;
case 14:
_DoPrint ();
return true;
case 16:
((_HYTextBox*)GetObject(0))->_DoUndo(true);
return true;
case 17:
((_HYTextBox*)GetObject(0))->_DoCut(true);
return true;
case 18:
((_HYTextBox*)GetObject(0))->_DoCopy(true);
return true;
case HY_WINDOW_MENU_ID_EDIT+5:
((_HYTextBox*)GetObject(0))->_DoSelectAll(true);
return true;
case 21:
SetStatusLine ("Canceling");
terminateExecution = true;
return true;
case 22: {
GtkWidget * suspendItem = gtk_item_factory_get_widget_by_action(menu_items,22);
if (!isSuspended) {
isSuspended = true;
SetStatusLine (empty,empty,empty,-1,HY_SL_SUSPEND);
gtk_label_set_text (GTK_LABEL (gtk_bin_get_child(GTK_BIN(suspendItem))), "Resume");
updateTimer = false;
while (isSuspended) {
gtk_main_iteration_do(true);
}
} else {
isSuspended = false;
SetStatusLine (empty,empty,empty,-1,HY_SL_RESUME);
gtk_label_set_text (GTK_LABEL (gtk_bin_get_child(GTK_BIN(suspendItem))), "Suspend execution");
timerStart += clock()-lastTimer;
updateTimer = true;
}
return true;
}
case 23:
ShowMessagesLog();
return true;
case 24:
RunStandardAnalyses();
return true;
case 25:
displayAbout(false);
return true;
case HY_WINDOW_MENU_ID_EDIT+4:
((_HYTextBox*)GetObject(0))->_DoClear (true,true);
return true;
case 27:
HandlePreferences (globalPreferencesList,"HYPHY Preferences");
return true;
case 29:
//WinExec ("hh HYPHY HELP.chm",SW_SHOWNORMAL);
return true;
case 30:
if (OpenBatchFile (false)) {
ExecuteBatchFile();
PopFilePath();
}
return true;
case 31:
((_HYTextBox*)GetObject(0))->_DoRedo(true);
return true;
case 15:
postWindowCloseEvent (GetID());
gtk_main_quit ();
return true;
case 60: // expression calculator
if (calculatorMode) {
_HYTextBox *ib = (_HYTextBox*)hyphyConsoleWindow->GetObject(1);
ib->SetText ("exit");
hyphyConsoleWindow->ProcessEvent (generateTextEditChangeEvent(ib->GetID(),2));
calculatorMode = false;
//ib->SetText (empty);
} else {
calculatorMode = true;
while(calculatorMode&&ExpressionCalculator()) {}
calculatorMode = false;
}
return true;
case 61: { // execute selection
ExecuteSelection();
return true;
}
case 70: // New Tree
NewTreeWindow(-1);
return true;
case 71: // New Model
NewModel(nil);
return true;
case 72: // New Chart
NewChartWindow();
return true;
case 73: // New Genetic Code
NewGeneticCodeTable(0);
return true;
case 74: // New Database
NewDatabaseFile(0);
return true;
case 80: // Open Batch File
if (OpenBatchFile()) {
ExecuteBatchFile ();
}
return true;
case 81: // Open Data File
OpenDataFile();
return true;
case 82: // Open Tree
OpenTreeFile();
return true;
case 83: // Open Text
OpenTextFile();
return true;
case 84: // Open Table
OpenTable ();
return true;
case 85: // Open SQLite database
OpenDatabaseFile (nil);
return true;
case HY_WINDOW_MENU_ID_FILE-2:
ShowObjectInspector ();
return true;
default: {
msel -= 1000;
if (msel<availablePostProcessors.lLength) {
ExecuteAPostProcessor (*(_String*)(*(_List*)availablePostProcessors(msel))(1));
return 0;
}
msel-=1000;
if (msel<(long)recentPaths.lLength) {
if (msel == -1) {
for (long mi=0; mi<recentFiles.lLength; mi++) {
GtkWidget * recFile = gtk_item_factory_get_widget_by_action(hyphyConsoleWindow->menu_items,2000+mi);
if (recFile) {
gtk_item_factory_delete_item(hyphyConsoleWindow->menu_items,gtk_item_factory_path_from_widget(recFile));
}
}
recentPaths.Clear();
recentFiles.Clear();
} else {
if (argFileName) {
*argFileName = *(_String*)recentPaths(msel);
} else {
argFileName = new _String (*(_String*)recentPaths(msel));
}
if (OpenBatchFile(false)) {
ExecuteBatchFile ();
}
}
return true;
}
return true;
}
}
return _HYTWindow::_ProcessMenuSelection(msel);
}
int main(int argc, char **argv)
{
int i, j, k, treeNo, sumLength;
char ch;
TTree **treeSet;
FILE *text_fv;
clock_t totalStart;
double totalSecs, scale, sum;
char *ancestor;
totalStart = clock();
ReadParams(argc, argv);
if (rateHetero == CodonRates && invariableSites) {
fprintf(stderr, "Invariable sites model cannot be used with codon rate heterogeneity.\n");
exit(4);
}
if (writeAncestors && fileFormat == NEXUSFormat) {
fprintf(stderr, "Warning - When writing ancestral sequences, relaxed PHYLIP format is used.\n");
}
if (writeAncestors && maxPartitions > 1) {
fprintf(stderr, "Writing ancestral sequences can only be used for a single partition.\n");
exit(4);
}
if (!userSeed)
randomSeed = CreateSeed();
SetSeed(randomSeed);
if (!quiet)
PrintTitle();
numTrees = OpenTreeFile();
/* if (!treeFile) { */
ReadFileParams();
/*} */
if ((ancestorSeq>0 && !hasAlignment) || ancestorSeq>numSequences) {
fprintf(stderr, "Bad ancestral sequence number: %d (%d sequences loaded)\n", ancestorSeq, numSequences);
exit(4);
}
if (textFile) {
if ( (text_fv=fopen(textFileName, "rt"))==NULL ) {
fprintf(stderr, "Error opening text file for insertion into output: '%s'\n", textFileName);
exit(4);
}
}
ancestor=NULL;
if (hasAlignment) {
AllocateMemory();
ReadFile();
if (numSites<0)
numSites=numAlignmentSites;
if (ancestorSeq>0) {
if (numSites!=numAlignmentSites) {
fprintf(stderr, "Ancestral sequence is of a different length to the simulated sequences (%d)\n", numAlignmentSites);
exit(4);
}
ancestor=sequences[ancestorSeq-1];
}
} else if (numSites<0)
numSites=1000;
SetModel(model);
numTaxa=-1;
scale=1.0;
treeSet = (TTree **)malloc(sizeof(TTree **) * maxPartitions);
if (treeSet==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
partitionLengths = (int *)malloc(sizeof(int) * maxPartitions);
if (partitionLengths==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
partitionRates = (double *)malloc(sizeof(double) * maxPartitions);
if (partitionRates==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
for (i = 0; i < maxPartitions; i++) {
if ((treeSet[i]=NewTree())==NULL) {
fprintf(stderr, "Out of memory\n");
exit(5);
}
}
CreateRates();
treeNo=0;
do {
partitionLengths[0] = -1;
ReadTree(tree_fv, treeSet[0], treeNo+1, 0, NULL, &partitionLengths[0], &partitionRates[0]);
if (treeNo==0) {
numTaxa=treeSet[0]->numTips;
if (!quiet)
fprintf(stderr, "Random number generator seed: %ld\n\n", randomSeed);
if (fileFormat == NEXUSFormat) {
fprintf(stdout, "#NEXUS\n");
fprintf(stdout, "[\nGenerated by %s %s\n\n", PROGRAM_NAME, VERSION_NUMBER);
PrintVerbose(stdout);
fprintf(stdout, "]\n\n");
}
} else if (treeSet[0]->numTips != numTaxa) {
fprintf(stderr, "All trees must have the same number of tips.\n");
exit(4);
}
if (maxPartitions == 1) {
if (partitionLengths[0] != -1) {
fprintf(stderr, "\nWARNING: The treefile contained partion lengths but only one partition\n");
fprintf(stderr, "was specified.\n");
}
partitionLengths[0] = numSites;
}
sumLength = partitionLengths[0];
i = 1;
while (sumLength < numSites && i <= maxPartitions) {
if (!IsTreeAvail(tree_fv)) {
fprintf(stderr, "\nA set of trees number %d had less partition length (%d) than\n", treeNo + 1, sumLength);
fprintf(stderr, "was required to make a sequence of length %d.\n", numSites);
exit(4);
}
ReadTree(tree_fv, treeSet[i], treeNo+1, treeSet[0]->numTips, treeSet[0]->names,
&partitionLengths[i], &partitionRates[i]);
if (treeSet[i]->numTips != numTaxa) {
fprintf(stderr, "All trees must have the same number of tips.\n");
exit(4);
}
sumLength += partitionLengths[i];
i++;
}
if (i > maxPartitions) {
fprintf(stderr, "\nA set of trees number %d had more partitions (%d) than\n", treeNo + 1, i);
fprintf(stderr, "was specified in the user options (%d).\n", maxPartitions);
}
numPartitions = i;
if (sumLength != numSites) {
fprintf(stderr, "The sum of the partition lengths in the treefile does not equal\n");
fprintf(stderr, "the specified number of sites.\n");
exit(4);
}
for (i = 0; i < numPartitions; i++)
CreateSequences(treeSet[i], partitionLengths[i]);
if (numPartitions > 1) {
sum = 0.0;
for (i = 0; i < numPartitions; i++)
sum += partitionRates[i] * partitionLengths[i];
for (i = 0; i < numPartitions; i++)
partitionRates[i] *= numSites / sum;
}
if (treeNo==0 && verbose && !quiet) {
PrintVerbose(stderr);
InitProgressBar(numTrees*numDatasets);
DrawProgressBar();
}
for (i=0; i<numDatasets; i++) {
SetCategories();
k = 0;
for (j = 0; j < numPartitions; j++) {
scale = partitionRates[j];
if (scaleTrees) {
if (!treeSet[j]->rooted) {
fprintf(stderr, "To scale tree length, they must be rooted and ultrametric.\n");
exit(4);
}
scale *= treeScale/treeSet[j]->totalLength;
} else if (scaleBranches)
scale *= branchScale;
EvolveSequences(treeSet[j], k, partitionLengths[j], scale, ancestor);
k += partitionLengths[j];
}
if (writeAncestors)
WriteAncestralSequences(stdout, treeSet[0]);
else
WriteSequences(stdout, (numTrees > 1 ? treeNo+1 : -1), (numDatasets > 1 ? i+1 : -1), treeSet, partitionLengths);
if (writeRates) {
WriteRates(stderr);
}
if (textFile) {
while (!feof(text_fv)) {
ch = fgetc(text_fv);
if (!feof(text_fv))
fputc(ch, stdout);
}
fputc('\n', stdout);
rewind(text_fv);
}
if (verbose && !quiet)
ProgressBar();
}
for (i = 0; i < numPartitions; i++)
DisposeTree(treeSet[i]);
treeNo++;
} while (IsTreeAvail(tree_fv));
/* for (i = 0; i < maxPartitions; i++)
FreeTree(treeSet[i]); */
if (treeFile)
fclose(tree_fv);
if (textFile)
fclose(text_fv);
totalSecs = (double)(clock() - totalStart) / CLOCKS_PER_SEC;
if (!quiet) {
fprintf(stderr, "Time taken: %G seconds\n", totalSecs);
if (verboseMemory)
fprintf(stderr, "Total memory used: %ld\n", totalMem);
}
return 0;
}