void
gioInitializeDescriptor (GioDescriptor *descriptor) {
descriptor->serial.parameters = NULL;
initializeOptions(&descriptor->serial.options);
descriptor->serial.options.inputTimeout = 100;
descriptor->usb.channelDefinitions = NULL;
initializeOptions(&descriptor->usb.options);
descriptor->usb.options.inputTimeout = 1000;
descriptor->usb.options.outputTimeout = 1000;
descriptor->bluetooth.channelNumber = 0;
initializeOptions(&descriptor->bluetooth.options);
descriptor->bluetooth.options.inputTimeout = 100;
}
void
MirfoxData::initializeMirfoxData()
{
initializeMirandaAccounts(); //must be before initializeMirandaContacts
initializeMirandaContacts();
initializeOptions();
}
void
interactive() {
char *sbmlFilename;
char *select;
int quit;
SBMLDocument_t *d = NULL;
Model_t *m = NULL;
odeModel_t *om = NULL;
cvodeData_t * data = NULL;
integratorInstance_t *ii = NULL;
cvodeSettings_t *set = NULL;
printf("\n\nWelcome to the simple SBML ODE solver.\n");
printf("You have entered the interactive mode.\n");
printf("All other commandline options have been ignored.\n");
printf("Have fun!\n\n");
initializeOptions();
/* reset steady state */
Opt.SteadyState = 0;
/* activate printing of results to XMGrace */
Opt.Xmgrace = 1;
/* activate printing integrator messages */
Opt.PrintMessage = 1;
/* deactivate on the fly printing of results */
Opt.PrintOnTheFly = 0;
sbmlFilename = concat(Opt.ModelPath, Opt.ModelFile);
if ( (d = parseModelWithArguments(sbmlFilename)) == 0 )
{
Warn(stderr, "%s:%d interactive(): Can't parse Model >%s<",
__FILE__, __LINE__, sbmlFilename);
d = loadFile();
}
/* load models and default settings */
m = SBMLDocument_getModel(d);
om = ODEModel_create(m);
set = CvodeSettings_create();
SolverError_dumpAndClearErrors();
quit = 0;
data = NULL;
while ( quit == 0 ) {
printf("\n");
printf("Press (h) for instructions or (q) to quit.\n");
printf("> ");
select = get_line( stdin );
select = util_trim(select);
printf("\n");
if( strcmp(select,"l") == 0 ) {
/* free all existing structures */
if ( om != NULL )
ODEModel_free(data->model);
if ( d != NULL )
SBMLDocument_free(d);
if ( ii != NULL )
IntegratorInstance_free(ii);
/* load a new file */
d = loadFile();
/* load new models */
m = SBMLDocument_getModel(d);
om = ODEModel_create(m);
SolverError_dumpAndClearErrors();
}
if(strcmp(select,"h")==0)
printMenu();
if(strcmp(select,"s")==0)
printModel(m, stdout);
if(strcmp(select,"c")==0)
printSpecies(m, stdout);
if(strcmp(select,"r")==0)
printReactions(m, stdout);
if(strcmp(select,"o")==0)
printODEs(om, stdout);
/* integrate interface functions, asks for time and printsteps */
if(strcmp(select,"i")==0){
ii = callIntegrator(om, set);
SolverError_dumpAndClearErrors();
}
if(strcmp(select,"x")==0){
if ( Opt.Xmgrace == 1 ) {
Opt.Xmgrace = 0;
printf(" Printing results to stdout\n");
}
else if ( Opt.Xmgrace == 0 ) {
Opt.Xmgrace = 1;
printf(" Printing results to XMGrace\n");
}
}
if(strcmp(select,"st")==0)
printConcentrationTimeCourse(ii->data, stdout);
if(strcmp(select,"jt")==0)
printJacobianTimeCourse(ii->data, stdout);
if(strcmp(select,"ot")==0)
printOdeTimeCourse(ii->data, stdout);
if(strcmp(select,"rt")==0)
printReactionTimeCourse(ii->data, m, stdout);
if(strcmp(select,"xp")==0)
printPhase(ii->data);
if(strcmp(select,"set")==0)
setValues(m);
if(strcmp(select,"ss")==0){
if ( Opt.SteadyState == 1 ) {
Opt.SteadyState = 0;
printf(" Not checking for steady states during integration.\n");
}
else if ( Opt.SteadyState == 0 ) {
Opt.SteadyState = 1;
printf(" Checking for steady states during integration.\n");
}
}
if(strcmp(select,"uj")==0){
if ( Opt.Jacobian == 1 ) {
Opt.Jacobian = 0;
printf(" Using CVODE's internal approximation\n");
printf(" of the jacobian matrix for integration\n");
}
else if ( Opt.Jacobian == 0 ) {
Opt.Jacobian = 1;
printf(" Using automatically generated\n");
printf(" jacobian matrix for integration\n");
}
}
if(strcmp(select,"gf")==0)
setFormat();
if(strcmp(select,"rg")==0) {
drawModel(m, sbmlFilename, Opt.GvFormat);
SolverError_dumpAndClearErrors();
}
if(strcmp(select,"jg")==0){
if ( ii == NULL ) {
data = CvodeData_create(om);
CvodeData_initialize(data, set, om, 0);
drawJacoby(data, sbmlFilename, Opt.GvFormat);
SolverError_dumpAndClearErrors();
CvodeData_free(data);
}
else {
drawJacoby(ii->data, sbmlFilename, Opt.GvFormat);
SolverError_dumpAndClearErrors();
}
}
if(strcmp(select,"j")==0) {
if ( om->jacob == NULL )
ODEModel_constructJacobian(om);
printJacobian(om, stdout);
}
if(strcmp(select,"q")==0)
quit = 1;
}
if ( ii != NULL )
IntegratorInstance_free(ii);
if ( om != NULL )
ODEModel_free(om);
SBMLDocument_free(d);
SolverError_dumpAndClearErrors();
printf("\n\nGood Bye. Thx for using.\n\n");
}
void
decodeCML (int argc, char *argv[])
{
initializeOptions();
processOptions(argc, argv);
}
BOOL CALLBACK ConfigDialog::run_dlgProc(UINT Message, WPARAM wParam, LPARAM lParam)
{
LRESULT result;
switch (Message)
{
case WM_INITDIALOG :
{
initializeOptions();
goToCenter();
Edit_LimitText(GetDlgItem(_hSelf, IDC_MAXDISPLAYFILES), 7);
Edit_LimitText(GetDlgItem(_hSelf, IDC_MAXTRAVERSEFILES), 7);
Edit_LimitText(GetDlgItem(_hSelf, IDC_SEARCHCONTEXTPATH), MAX_PATH);
initTooltips();
return TRUE;
}
case WM_COMMAND :
{
switch (LOWORD(wParam))
{
case IDC_RADIOSORTREMEMBER:
case IDC_RADIOSORTINDEX:
case IDC_RADIOSORTPATH:
case IDC_RADIOSORTFILENAME:
{
enableOrDisableSortCheckBoxes();
break;
}
case IDC_CHECKSORTDESCENDING :
{
_options->activeReversedSortOrder = (BST_CHECKED != ::SendDlgItemMessage(_hSelf, IDC_CHECKOVERRIDESORTWHENTABBING, BM_GETCHECK, 0, 0));
break;
}
case IDC_CHECKDIALOGFORCTRLTAB :
{
bool checked = BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKDIALOGFORCTRLTAB, BM_GETCHECK, 0, 0);
EnableWindow(GetDlgItem(_hSelf, IDC_CHECKREVERTSORTORDERDURINGTABBING), checked);
break;
}
case IDC_CHECKCONFIGURESEARCHCONTEXT:
{
bool isChecked = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKCONFIGURESEARCHCONTEXT, BM_GETCHECK, 0, 0));
EnableWindow(GetDlgItem(_hSelf, IDC_SEARCHCONTEXTPATH), isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_MAXTRAVERSEFILES), isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_MAXDISPLAYFILES), isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_CHECKINCLUDEINDEX), !isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_CHECKINCLUDEVIEW), !isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_RADIOSORTINDEX), !isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_CHECKONLYCURRENTVIEW), !isChecked);
EnableWindow(GetDlgItem(_hSelf, IDC_CHECKSEPARATECOLUMNFORVIEW), !isChecked);
if(BST_CHECKED && ::SendDlgItemMessage(_hSelf, IDC_RADIOSORTINDEX, BM_GETCHECK, 0, 0))
{
::SendDlgItemMessage(_hSelf, IDC_RADIOSORTFILENAME, BM_SETCHECK, BST_CHECKED, 0);
}
else if(!BST_CHECKED && ::SendDlgItemMessage(_hSelf, IDC_RADIOSORTINDEX, BM_GETCHECK, 0, 0))
{
::SendDlgItemMessage(_hSelf, IDC_RADIOSORTREMEMBER, BM_SETCHECK, BST_UNCHECKED, 0);
::SendDlgItemMessage(_hSelf, IDC_RADIOSORTFILENAME, BM_SETCHECK, BST_UNCHECKED, 0);
::SendDlgItemMessage(_hSelf, IDC_RADIOSORTPATH, BM_SETCHECK, BST_UNCHECKED, 0);
}
break;
}
case IDC_CHECKAUTOSIZECOLUMNS:
{
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKAUTOSIZECOLUMNS, BM_GETCHECK, 0, 0);
EnableWindow(GetDlgItem(_hSelf, IDC_CHECKAUTOSIZEWINDOW), BST_CHECKED == result);
break;
}
case IDOK :
{
tstring error = _T("");
_options->searchFlags = 0;
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKSTARTONLY, BM_GETCHECK, 0, 0);
if (BST_CHECKED == result)
_options->searchFlags |= SEARCHFLAG_STARTONLY;
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKCASE, BM_GETCHECK, 0, 0);
if (BST_CHECKED == result)
_options->searchFlags |= SEARCHFLAG_CASESENSITIVE;
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKINCLUDEPATH, BM_GETCHECK, 0, 0);
if (BST_CHECKED == result)
_options->searchFlags |= SEARCHFLAG_INCLUDEPATH;
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKINCLUDEFILENAME, BM_GETCHECK, 0, 0);
if (BST_CHECKED == result)
_options->searchFlags |= SEARCHFLAG_INCLUDEFILENAME;
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKINCLUDEINDEX, BM_GETCHECK, 0, 0);
if (BST_CHECKED == result)
_options->searchFlags |= SEARCHFLAG_INCLUDEINDEX;
result = ::SendDlgItemMessage(_hSelf, IDC_CHECKINCLUDEVIEW, BM_GETCHECK, 0, 0);
if (BST_CHECKED == result)
_options->searchFlags |= SEARCHFLAG_INCLUDEVIEW;
_options->hasConfiguredContext = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKCONFIGURESEARCHCONTEXT, BM_GETCHECK, 0, 0));
if(
(
!_options->hasConfiguredContext
&& !(_options->searchFlags & SEARCHFLAG_INCLUDEPATH)
&& !(_options->searchFlags & SEARCHFLAG_INCLUDEFILENAME)
&& !(_options->searchFlags & SEARCHFLAG_INCLUDEINDEX)
&& !(_options->searchFlags & SEARCHFLAG_INCLUDEVIEW)
)
|| (
_options->hasConfiguredContext
&& !(_options->searchFlags & SEARCHFLAG_INCLUDEPATH)
&& !(_options->searchFlags & SEARCHFLAG_INCLUDEFILENAME)
)
){
tstring tmpMsg = _T("- Must select at least one item to include in your search");
error.length() > 0
? error.append(_T("\r\n")).append(tmpMsg)
: error.append(tmpMsg);
}
_options->disabledSelectedSortOrder = NONE;
if (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_RADIOSORTREMEMBER, BM_GETCHECK, 0, 0))
{
if (IsWindowEnabled(GetDlgItem(_hSelf, IDC_RADIOSORTREMEMBER)))
_options->defaultSortOrder = ALWAYSREMEMBER;
else
_options->disabledSelectedSortOrder = ALWAYSREMEMBER;
}
_options->reversedSortOrder = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKSORTDESCENDING, BM_GETCHECK, 0, 0));
_options->resetSortOrder = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKRESETSORTORDER, BM_GETCHECK, 0, 0));
if (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_RADIOSORTFILENAME, BM_GETCHECK, 0, 0))
{
if (IsWindowEnabled(GetDlgItem(_hSelf, IDC_RADIOSORTFILENAME)))
{
_options->activeSortOrder = FILENAME;
_options->defaultSortOrder = FILENAME;
}
else
_options->disabledSelectedSortOrder = FILENAME;
}
if (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_RADIOSORTPATH, BM_GETCHECK, 0, 0))
{
if (IsWindowEnabled(GetDlgItem(_hSelf, IDC_RADIOSORTPATH)))
{
_options->activeSortOrder = PATH;
_options->defaultSortOrder = PATH;
}
else
_options->disabledSelectedSortOrder = PATH;
}
if (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_RADIOSORTINDEX, BM_GETCHECK, 0, 0))
{
if (IsWindowEnabled(GetDlgItem(_hSelf, IDC_RADIOSORTINDEX)))
{
_options->activeSortOrder = INDEX;
_options->defaultSortOrder = INDEX;
}
else
_options->disabledSelectedSortOrder = INDEX;
}
_options->overrideSortWhenTabbing = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKOVERRIDESORTWHENTABBING, BM_GETCHECK, 0, 0));
_options->revertSortWhenTabbing = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKREVERTSORTORDERDURINGTABBING, BM_GETCHECK, 0, 0));
_options->onlyUseCurrentView = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKONLYCURRENTVIEW, BM_GETCHECK, 0, 0));
_options->autoSizeColumns = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKAUTOSIZECOLUMNS, BM_GETCHECK, 0, 0));
_options->autoSizeWindow = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKAUTOSIZEWINDOW, BM_GETCHECK, 0, 0));
_options->columnForView = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKSEPARATECOLUMNFORVIEW, BM_GETCHECK, 0, 0));
_options->showDialogForCtrlTab = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKDIALOGFORCTRLTAB, BM_GETCHECK, 0, 0));
_options->useHomeForEdit = (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKUSEHOMEFOREDIT, BM_GETCHECK, 0, 0));
if(BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKWILDCARD, BM_GETCHECK, 0, 0))
_options->searchFlags |= SEARCHFLAG_INCLUDEWILDCARD;
if (BST_CHECKED == ::SendDlgItemMessage(_hSelf, IDC_CHECKCASE, BM_GETCHECK, 0, 0))
_options->searchFlags |= SEARCHFLAG_CASESENSITIVE;
bool isNumber = true;
TCHAR bufMaxs[20];
GetDlgItemText(_hSelf, IDC_MAXTRAVERSEFILES, bufMaxs, MAX_PATH);
tstring tmpMaxs = bufMaxs;
if(tmpMaxs.length() > 0 && is_number(tmpMaxs))
{
_options->maxTraverseFiles = _tstoi(tmpMaxs.c_str());
}
else
{
tstring tmpMsg = _T("- Maximum files traversed is not a valid number");
error.length() > 0
? error.append(_T("\r\n")).append(tmpMsg)
: error.append(tmpMsg);
isNumber = false;
}
GetDlgItemText(_hSelf, IDC_MAXDISPLAYFILES, bufMaxs, MAX_PATH);
tmpMaxs = bufMaxs;
if(tmpMaxs.length() > 0 && is_number(tmpMaxs))
{
_options->maxDisplayFiles = _tstoi(tmpMaxs.c_str());
}
else
{
tstring tmpMsg = _T("- Maximum files displayed is not a valid number");
error.length() > 0
? error.append(_T("\r\n")).append(tmpMsg)
: error.append(tmpMsg);
isNumber = false;
}
if(isNumber && _options->maxTraverseFiles < _options->maxDisplayFiles)
{
tstring tmpMsg = _T("- Max traverse files must be more than max display files.");
error.length() > 0
? error.append(_T("\r\n")).append(tmpMsg)
: error.append(tmpMsg);
}
TCHAR tmpPath[MAX_PATH];
result = ::GetDlgItemText(_hSelf, IDC_SEARCHCONTEXTPATH, tmpPath, MAX_PATH);
tstring tstrPath = tmpPath;
if(_options->hasConfiguredContext
&& (tstrPath.length() > 0))
_options->configuredContextPath = (tstrPath.back() == _T('\\')) ? tstrPath : tstrPath.append(_T("\\"));
if(_options->hasConfiguredContext
&& !(_options->ConfiguredContextPathIsValid())
){
tstring tmpMsg = _T("- Context path is invalid. Please provide a valid context path.");
error.length() > 0
? error.append(_T("\r\n")).append(tmpMsg)
: error.append(tmpMsg);
}
if(error.length() > 0)
{
MessageBox(_hSelf, error.c_str(), _T("Error"), MB_OK);
return TRUE;
}
g_filesNeedToBeReloaded(
(_tcscmp(contextPathOnInit.c_str(), _options->configuredContextPath.c_str()) != 0)
|| (!contextConfiguredOnInit && _options->hasConfiguredContext));
redisplaySwitchDialog();
}
case IDCANCEL :
{
if (_isModal)
EndDialog(_hSelf, 0);
else
display(FALSE);
redisplaySwitchDialog();
return TRUE;
}
case IDABORT :
case IDCLOSE :
{
redisplaySwitchDialog();
}
default :
break;
}
}
}
return FALSE;
}
OptionS *
decodeCML(int argc, char *argv[]) {
initializeOptions(argv[0]);
processOptions(argc, argv);
return (&OptS);
}