int Molecule::get_new_frames() {
int newframes = 0;
// add a new frame if there are frames available in the I/O queue
if (next_frame())
newframes = 1;
// If an IMD simulation is in progress, store the forces in the current
// timestep and send them to the simulation. Otherwise, just toss them.
if (app->imd_connected(id())) {
// Add persistent forces to regular forces
int ii;
for (ii=0; ii<persistent_force_indices.num(); ii++)
force_indices.append(persistent_force_indices[ii]);
for (ii=0; ii<persistent_force_vectors.num(); ii++)
force_vectors.append(persistent_force_vectors[ii]);
// Clear old forces out of the timestep
Timestep *ts = current();
if (ts && ts->force) {
memset(ts->force, 0, 3*nAtoms*sizeof(float));
}
// Check for atoms forced last time that didn't show up this time.
// XXX order N^2 in number of applied forces; could be easily improved.
// But N now is usually 1 or 2.
ResizeArray<int> zero_force_indices;
ResizeArray<float> zero_forces;
for(ii=0; ii<last_force_indices.num(); ii++) {
int j;
int index_missing=1;
for (j=0; j<force_indices.num(); j++) {
if (force_indices[j]==last_force_indices[ii]) {
index_missing=0;
break;
}
}
if (index_missing) {
// this one didn't show up this time
zero_force_indices.append(last_force_indices[ii]);
zero_forces.append(0);
zero_forces.append(0);
zero_forces.append(0);
}
}
if (zero_force_indices.num()) {
// There some atoms forced last time that didn't show up this time.
app->imd_sendforces(zero_force_indices.num(), &(zero_force_indices[0]),
&(zero_forces[0]));
}
// now clear the last forces so we don't send them again
last_force_indices.clear();
// Set/send forces if we got any
if (force_indices.num()) {
if (ts) {
if (!ts->force) {
ts->force = new float[3*nAtoms];
memset(ts->force, 0, 3*nAtoms*sizeof(float));
}
for (int i=0; i<force_indices.num(); i++) {
int ind = force_indices[i];
ts->force[3*ind ] += force_vectors[3*i ];
ts->force[3*ind+1] += force_vectors[3*i+1];
ts->force[3*ind+2] += force_vectors[3*i+2];
}
}
// XXX If we send multiple forces for the same atom, NAMD will keep only
// the last force. We therefore have to sum multiple contributions to the
// same atom before sending. Annoying.
ResizeArray<float> summed_forces;
int i;
for (i=0; i<force_indices.num(); i++) {
int ind = force_indices[i];
summed_forces.append(ts->force[3*ind ]);
summed_forces.append(ts->force[3*ind+1]);
summed_forces.append(ts->force[3*ind+2]);
}
app->imd_sendforces(force_indices.num(), &(force_indices[0]),
&(summed_forces[0]));
// save the force indices before clearing them
for (i=0; i<force_indices.num(); i++) {
last_force_indices.append(force_indices[i]);
}
// now clear the force indices
force_indices.clear();
force_vectors.clear();
}
}
// Inform the top level class that background processing
// is going on to prevent the CPU throttling code from activating
if (newframes > 0)
app->background_processing_set();
return newframes;
}
bool atParagraphSeparator() const
{
// Within a cue, paragraph boundaries are only denoted by Type B characters,
// such as U+000A LINE FEED (LF), U+0085 NEXT LINE (NEL), and U+2029 PARAGRAPH SEPARATOR.
return WTF::Unicode::category(current()) & WTF::Unicode::Separator_Paragraph;
}
/**
* Rearranges the atomic entities in this container in a way that connected
* entities are stored in the right order and direction.
* Non-recoursive. Only affects atomic entities in this container.
*
* @retval true all contours were closed
* @retval false at least one contour is not closed
*/
bool RS_EntityContainer::optimizeContours() {
RS_DEBUG->print("RS_EntityContainer::optimizeContours");
RS_Vector current(false);
RS_Vector start(false);
RS_EntityContainer tmp;
bool changed = false;
bool closed = true;
for (uint ci=0; ci<count(); ++ci) {
RS_Entity* e1=entityAt(ci);
if (e1!=NULL && e1->isEdge() && !e1->isContainer() &&
!e1->isProcessed()) {
RS_AtomicEntity* ce = (RS_AtomicEntity*)e1;
// next contour start:
ce->setProcessed(true);
tmp.addEntity(ce->clone());
current = ce->getEndpoint();
start = ce->getStartpoint();
// find all connected entities:
bool done;
do {
done = true;
for (uint ei=0; ei<count(); ++ei) {
RS_Entity* e2=entityAt(ei);
if (e2!=NULL && e2->isEdge() && !e2->isContainer() &&
!e2->isProcessed()) {
RS_AtomicEntity* e = (RS_AtomicEntity*)e2;
if (e->getStartpoint().distanceTo(current) <
1.0e-4) {
e->setProcessed(true);
tmp.addEntity(e->clone());
current = e->getEndpoint();
done=false;
} else if (e->getEndpoint().distanceTo(current) <
1.0e-4) {
e->setProcessed(true);
RS_AtomicEntity* cl = (RS_AtomicEntity*)e->clone();
cl->reverse();
tmp.addEntity(cl);
current = cl->getEndpoint();
changed = true;
done=false;
}
}
}
if (!done) {
changed = true;
}
} while (!done);
if (current.distanceTo(start)>1.0e-4) {
closed = false;
}
}
}
// remove all atomic entities:
bool done;
do {
done = true;
for (RS_Entity* en=firstEntity(); en!=NULL; en=nextEntity()) {
if (!en->isContainer()) {
removeEntity(en);
done = false;
break;
}
}
} while (!done);
// add new sorted entities:
for (RS_Entity* en=tmp.firstEntity(); en!=NULL; en=tmp.nextEntity()) {
en->setProcessed(false);
addEntity(en->clone());
}
RS_DEBUG->print("RS_EntityContainer::optimizeContours: OK");
return closed;
}
int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
try {
int pid;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
for(int i=0;i<num;i++){
if (m->control_pressed) { return 0; }
//read next sequence
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
string tempBuf = buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
istringstream iss (tempBuf,istringstream::in);
delete buf4;
Sequence current(iss);
if (current.getName() != "") {
int num = 1;
if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your name or count file, please correct." << endl; m->control_pressed = true; }
else { num = it->second; }
}
//for each sequence this sequence represents
for (int j = 0; j < num; j++) {
startPosition.push_back(current.getStartPos());
endPosition.push_back(current.getEndPos());
seqLength.push_back(current.getNumBases());
ambigBases.push_back(current.getAmbigBases());
longHomoPolymer.push_back(current.getLongHomoPolymer());
}
string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
//output to file
length = outputString.length();
char* buf3 = new char[length];
memcpy(buf3, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
delete buf3;
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
exit(1);
}
}
void ReorderBuildStrategy::_handleMatchNoDedup( ResultDetails* resultDetails ) {
DiskLoc loc = _cursor->currLoc();
_scanAndOrder->add( current( false, resultDetails ),
_parsedQuery.showDiskLoc() ? &loc : 0 );
}
void RelocIterator::print_current() {
if (!has_current()) {
tty->print_cr("(no relocs)");
return;
}
tty->print("relocInfo@" INTPTR_FORMAT " [type=%d(%s) addr=" INTPTR_FORMAT,
_current, type(), reloc_type_string((relocInfo::relocType) type()), _addr);
if (current()->format() != 0)
tty->print(" format=%d", current()->format());
if (datalen() == 1) {
tty->print(" data=%d", data()[0]);
} else if (datalen() > 0) {
tty->print(" data={");
for (int i = 0; i < datalen(); i++) {
tty->print("%04x", data()[i] & 0xFFFF);
}
tty->print("}");
}
tty->print("]");
switch (type()) {
case relocInfo::oop_type:
{
oop_Relocation* r = oop_reloc();
oop* oop_addr = NULL;
oop raw_oop = NULL;
oop oop_value = NULL;
if (code() != NULL || r->oop_index() == 0) {
oop_addr = r->oop_addr();
raw_oop = *oop_addr;
oop_value = r->oop_value();
}
tty->print_cr(" | [oop_addr=" INTPTR_FORMAT " *=" INTPTR_FORMAT " offset=%d]",
oop_addr, raw_oop, r->offset());
// Do not print the oop by default--we want this routine to
// work even during GC or other inconvenient times.
if (WizardMode && oop_value != NULL) {
tty->print("oop_value=" INTPTR_FORMAT ": ", oop_value);
oop_value->print_value_on(tty);
}
break;
}
case relocInfo::external_word_type:
case relocInfo::internal_word_type:
{
DataRelocation* r = (DataRelocation*) reloc();
tty->print(" | [target=" INTPTR_FORMAT "]", r->value()); //value==target
break;
}
case relocInfo::static_call_type:
case relocInfo::runtime_call_type:
{
CallRelocation* r = (CallRelocation*) reloc();
tty->print(" | [destination=" INTPTR_FORMAT "]", r->destination());
break;
}
case relocInfo::virtual_call_type:
{
virtual_call_Relocation* r = (virtual_call_Relocation*) reloc();
tty->print(" | [destination=" INTPTR_FORMAT " first_oop=" INTPTR_FORMAT " oop_limit=" INTPTR_FORMAT "]",
r->destination(), r->first_oop(), r->oop_limit());
break;
}
case relocInfo::static_stub_type:
{
static_stub_Relocation* r = (static_stub_Relocation*) reloc();
tty->print(" | [static_call=" INTPTR_FORMAT "]", r->static_call());
break;
}
}
tty->cr();
}
int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
try {
ofstream outSummary;
m->openOutputFile(sumFile, outSummary);
//print header if you are process 0
if (filePos->start == 0) {
outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
}
ifstream in;
m->openInputFile(filename, in);
in.seekg(filePos->start);
bool done = false;
int count = 0;
while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n"); }
Sequence current(in); m->gobble(in);
if (current.getName() != "") {
if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
int num = 1;
if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your name or count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
//for each sequence this sequence represents
for (int i = 0; i < num; i++) {
startPosition.push_back(current.getStartPos());
endPosition.push_back(current.getEndPos());
seqLength.push_back(current.getNumBases());
ambigBases.push_back(current.getAmbigBases());
longHomoPolymer.push_back(current.getLongHomoPolymer());
}
count++;
outSummary << current.getName() << '\t';
outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (in.eof()) { break; }
#endif
}
in.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
exit(1);
}
}
void GlutWindow::refreshTimer(int _val) {
current()->displayTimer(_val);
}
void GlutWindow::runTimer(int _val) {
current()->simTimer(_val);
}
void GlutWindow::refresh() {
current()->render();
}
void GlutWindow::mouseMove(int _x, int _y) {
current()->move(_x, _y);
}
void GlutWindow::mouseDrag(int _x, int _y) {
current()->drag(_x, _y);
}
QLayoutItem* next()
{
m_idx++;
return current();
}
void
threadmain(int argc, char *argv[])
{
int i, got, scr;
Text *t;
Rectangle r;
Flayer *nwhich;
getscreen(argc, argv);
iconinit();
initio();
scratch = alloc(100*RUNESIZE);
nscralloc = 100;
r = screen->r;
r.max.y = r.min.y+Dy(r)/5;
flstart(screen->clipr);
rinit(&cmd.rasp);
flnew(&cmd.l[0], gettext, 1, &cmd);
flinit(&cmd.l[0], r, font, cmdcols);
cmd.nwin = 1;
which = &cmd.l[0];
cmd.tag = Untagged;
outTs(Tversion, VERSION);
startnewfile(Tstartcmdfile, &cmd);
got = 0;
for(;;got = waitforio()){
if(hasunlocked && RESIZED())
resize();
if(got&(1<<RHost))
rcv();
if(got&(1<<RPlumb)){
for(i=0; cmd.l[i].textfn==0; i++)
;
current(&cmd.l[i]);
flsetselect(which, cmd.rasp.nrunes, cmd.rasp.nrunes);
type(which, RPlumb);
}
if(got&(1<<RKeyboard))
if(which)
type(which, RKeyboard);
else
kbdblock();
if(got&(1<<RMouse)){
if(hostlock==2 || !ptinrect(mousep->xy, screen->r)){
mouseunblock();
continue;
}
nwhich = flwhich(mousep->xy);
scr = which && ptinrect(mousep->xy, which->scroll);
if(mousep->buttons)
flushtyping(1);
if(mousep->buttons&1){
if(nwhich){
if(nwhich!=which)
current(nwhich);
else if(scr)
scroll(which, 1);
else{
t=(Text *)which->user1;
if(flselect(which)){
outTsl(Tdclick, t->tag, which->p0);
t->lock++;
}else if(t!=&cmd)
outcmd();
}
}
}else if((mousep->buttons&2) && which){
if(scr)
scroll(which, 2);
else
menu2hit();
}else if((mousep->buttons&4)){
if(scr)
scroll(which, 3);
else
menu3hit();
}
mouseunblock();
}
}
}
bool CGUIDialogContextMenu::OnContextButton(const std::string &type, const CFileItemPtr& item, CONTEXT_BUTTON button)
{
// Add Source doesn't require a valid share
if (button == CONTEXT_BUTTON_ADD_SOURCE)
{
if (CProfilesManager::GetInstance().IsMasterProfile())
{
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
}
else if (!CProfilesManager::GetInstance().GetCurrentProfile().canWriteSources() && !g_passwordManager.IsProfileLockUnlocked())
return false;
return CGUIDialogMediaSource::ShowAndAddMediaSource(type);
}
// buttons that are available on both sources and autosourced items
if (!item) return false;
switch (button)
{
case CONTEXT_BUTTON_EJECT_DRIVE:
return g_mediaManager.Eject(item->GetPath());
#ifdef HAS_DVD_DRIVE
case CONTEXT_BUTTON_PLAY_DISC:
return MEDIA_DETECT::CAutorun::PlayDisc(item->GetPath(), true, true); // restart
case CONTEXT_BUTTON_RESUME_DISC:
return MEDIA_DETECT::CAutorun::PlayDisc(item->GetPath(), true, false); // resume
case CONTEXT_BUTTON_EJECT_DISC:
g_mediaManager.ToggleTray(g_mediaManager.TranslateDevicePath(item->GetPath())[0]);
#endif
return true;
default:
break;
}
// the rest of the operations require a valid share
CMediaSource *share = GetShare(type, item.get());
if (!share) return false;
switch (button)
{
case CONTEXT_BUTTON_EDIT_SOURCE:
if (CProfilesManager::GetInstance().IsMasterProfile())
{
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
}
else if (!g_passwordManager.IsProfileLockUnlocked())
return false;
return CGUIDialogMediaSource::ShowAndEditMediaSource(type, *share);
case CONTEXT_BUTTON_REMOVE_SOURCE:
{
if (CProfilesManager::GetInstance().IsMasterProfile())
{
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
}
else
{
if (!CProfilesManager::GetInstance().GetCurrentProfile().canWriteSources() && !g_passwordManager.IsMasterLockUnlocked(false))
return false;
if (CProfilesManager::GetInstance().GetCurrentProfile().canWriteSources() && !g_passwordManager.IsProfileLockUnlocked())
return false;
}
// prompt user if they want to really delete the source
if (!CGUIDialogYesNo::ShowAndGetInput(CVariant{751}, CVariant{750}))
return false;
// check default before we delete, as deletion will kill the share object
std::string defaultSource(GetDefaultShareNameByType(type));
if (!defaultSource.empty())
{
if (share->strName == defaultSource)
ClearDefault(type);
}
CMediaSourceSettings::GetInstance().DeleteSource(type, share->strName, share->strPath);
return true;
}
case CONTEXT_BUTTON_SET_DEFAULT:
if (CProfilesManager::GetInstance().GetCurrentProfile().canWriteSources() && !g_passwordManager.IsProfileLockUnlocked())
return false;
else if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
// make share default
SetDefault(type, share->strName);
return true;
case CONTEXT_BUTTON_CLEAR_DEFAULT:
if (CProfilesManager::GetInstance().GetCurrentProfile().canWriteSources() && !g_passwordManager.IsProfileLockUnlocked())
return false;
else if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
// remove share default
ClearDefault(type);
return true;
case CONTEXT_BUTTON_SET_THUMB:
{
if (CProfilesManager::GetInstance().GetCurrentProfile().canWriteSources() && !g_passwordManager.IsProfileLockUnlocked())
return false;
else if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
// setup our thumb list
CFileItemList items;
// add the current thumb, if available
if (!share->m_strThumbnailImage.empty())
{
CFileItemPtr current(new CFileItem("thumb://Current", false));
current->SetArt("thumb", share->m_strThumbnailImage);
current->SetLabel(g_localizeStrings.Get(20016));
items.Add(current);
}
else if (item->HasArt("thumb"))
{ // already have a thumb that the share doesn't know about - must be a local one, so we mayaswell reuse it.
CFileItemPtr current(new CFileItem("thumb://Current", false));
current->SetArt("thumb", item->GetArt("thumb"));
current->SetLabel(g_localizeStrings.Get(20016));
items.Add(current);
}
// see if there's a local thumb for this item
std::string folderThumb = item->GetFolderThumb();
if (XFILE::CFile::Exists(folderThumb))
{
CFileItemPtr local(new CFileItem("thumb://Local", false));
local->SetArt("thumb", folderThumb);
local->SetLabel(g_localizeStrings.Get(20017));
items.Add(local);
}
// and add a "no thumb" entry as well
CFileItemPtr nothumb(new CFileItem("thumb://None", false));
nothumb->SetIconImage(item->GetIconImage());
nothumb->SetLabel(g_localizeStrings.Get(20018));
items.Add(nothumb);
std::string strThumb;
VECSOURCES shares;
g_mediaManager.GetLocalDrives(shares);
if (!CGUIDialogFileBrowser::ShowAndGetImage(items, shares, g_localizeStrings.Get(1030), strThumb))
return false;
if (strThumb == "thumb://Current")
return true;
if (strThumb == "thumb://Local")
strThumb = folderThumb;
if (strThumb == "thumb://None")
strThumb = "";
if (!share->m_ignore)
{
CMediaSourceSettings::GetInstance().UpdateSource(type,share->strName,"thumbnail",strThumb);
CMediaSourceSettings::GetInstance().Save();
}
else if (!strThumb.empty())
{ // this is some sort of an auto-share, so store in the texture database
CTextureDatabase db;
if (db.Open())
db.SetTextureForPath(item->GetPath(), "thumb", strThumb);
}
CGUIMessage msg(GUI_MSG_NOTIFY_ALL,0,0,GUI_MSG_UPDATE_SOURCES);
g_windowManager.SendThreadMessage(msg);
return true;
}
case CONTEXT_BUTTON_ADD_LOCK:
{
// prompt user for mastercode when changing lock settings) only for default user
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
std::string strNewPassword = "";
if (!CGUIDialogLockSettings::ShowAndGetLock(share->m_iLockMode,strNewPassword))
return false;
// password entry and re-entry succeeded, write out the lock data
share->m_iHasLock = 2;
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "lockcode", strNewPassword);
strNewPassword = StringUtils::Format("%i", share->m_iLockMode);
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "lockmode", strNewPassword);
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "badpwdcount", "0");
CMediaSourceSettings::GetInstance().Save();
CGUIMessage msg(GUI_MSG_NOTIFY_ALL,0,0,GUI_MSG_UPDATE_SOURCES);
g_windowManager.SendThreadMessage(msg);
return true;
}
case CONTEXT_BUTTON_RESET_LOCK:
{
// prompt user for profile lock when changing lock settings
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "badpwdcount", "0");
CMediaSourceSettings::GetInstance().Save();
CGUIMessage msg(GUI_MSG_NOTIFY_ALL,0,0,GUI_MSG_UPDATE_SOURCES);
g_windowManager.SendThreadMessage(msg);
return true;
}
case CONTEXT_BUTTON_REMOVE_LOCK:
{
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
if (!CGUIDialogYesNo::ShowAndGetInput(CVariant{12335}, CVariant{750}))
return false;
share->m_iHasLock = 0;
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "lockmode", "0");
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "lockcode", "0");
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "badpwdcount", "0");
CMediaSourceSettings::GetInstance().Save();
CGUIMessage msg(GUI_MSG_NOTIFY_ALL,0,0,GUI_MSG_UPDATE_SOURCES);
g_windowManager.SendThreadMessage(msg);
return true;
}
case CONTEXT_BUTTON_REACTIVATE_LOCK:
{
bool maxRetryExceeded = false;
if (CSettings::GetInstance().GetInt(CSettings::SETTING_MASTERLOCK_MAXRETRIES) != 0)
maxRetryExceeded = (share->m_iBadPwdCount >= CSettings::GetInstance().GetInt(CSettings::SETTING_MASTERLOCK_MAXRETRIES));
if (!maxRetryExceeded)
{
// don't prompt user for mastercode when reactivating a lock
g_passwordManager.LockSource(type, share->strName, true);
return true;
}
return false;
}
case CONTEXT_BUTTON_CHANGE_LOCK:
{
if (!g_passwordManager.IsMasterLockUnlocked(true))
return false;
std::string strNewPW;
std::string strNewLockMode;
if (CGUIDialogLockSettings::ShowAndGetLock(share->m_iLockMode,strNewPW))
strNewLockMode = StringUtils::Format("%i",share->m_iLockMode);
else
return false;
// password ReSet and re-entry succeeded, write out the lock data
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "lockcode", strNewPW);
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "lockmode", strNewLockMode);
CMediaSourceSettings::GetInstance().UpdateSource(type, share->strName, "badpwdcount", "0");
CMediaSourceSettings::GetInstance().Save();
CGUIMessage msg(GUI_MSG_NOTIFY_ALL,0,0,GUI_MSG_UPDATE_SOURCES);
g_windowManager.SendThreadMessage(msg);
return true;
}
default:
break;
}
return false;
}
Path& Path::makeAbsolute()
{
return makeAbsolute(current());
}
void GlutWindow::specKeyEvent(int _key, int _x, int _y) {
current()->specKey(_key, _x, _y);
}
void
NetworkPrefsView::MessageReceived (BMessage * msg)
{
switch (msg->what)
{
case M_NETWORK_DEFAULTS:
if (fActiveNetwork.HasString ("name"))
vision_app->SetNetwork (fActiveNetwork.FindString ("name"), &fActiveNetwork);
fActiveNetwork = vision_app->GetNetwork ("defaults");
fNetworkMenu->MenuItem ()->SetLabel ("Defaults");
SetupDefaults (fActiveNetwork);
fDupeItem->SetEnabled (false);
fRemoveItem->SetEnabled (false);
break;
case M_CHOOSE_NETWORK:
{
BMenuItem *item (NULL);
msg->FindPointer ("source", reinterpret_cast < void **>(&item));
SaveCurrentNetwork ();
fActiveNetwork = vision_app->GetNetwork (item->Label ());
fNetworkMenu->MenuItem ()->SetLabel (item->Label ());
UpdatePersonalData (fActiveNetwork);
UpdateNetworkData (fActiveNetwork);
if (BMessenger (fServerPrefs).IsValid ())
fServerPrefs->SetNetworkData (&fActiveNetwork);
fDupeItem->SetEnabled (true);
fRemoveItem->SetEnabled (true);
}
break;
case M_ADD_NEW_NETWORK:
{
if (msg->HasString ("text"))
{
fNetPrompt = NULL;
BString network (msg->FindString ("text"));
network.RemoveAll (" ");
BMenu *menu (fNetworkMenu->Menu ());
for (int32 i = 0; i < menu->CountItems (); i++)
{
BMenuItem *item (menu->ItemAt (i));
if (item && network == item->Label ())
{
dynamic_cast < BInvoker * >(item)->Invoke ();
return;
}
}
BMessage newNet (VIS_NETWORK_DATA);
newNet.AddString ("name", network.String ());
vision_app->SetNetwork (network.String (), &newNet);
BMenuItem *item (new BMenuItem (network.String (), new BMessage (M_CHOOSE_NETWORK)));
menu->AddItem (item, 0);
item->SetTarget (this);
dynamic_cast < BInvoker * >(item)->Invoke ();
}
else
{
BString promptText = B_TRANSLATE("Network Name");
promptText += ": ";
fNetPrompt = new PromptWindow (BPoint (Window ()->Frame ().left + Window ()->Frame ().Width () / 2, Window ()->Frame ().top + Window ()->Frame ().Height () / 2),
promptText.String(), B_TRANSLATE("Add Network"), NULL, this, new BMessage (M_ADD_NEW_NETWORK), NULL, false);
fNetPrompt->Show ();
}
}
break;
case M_REMOVE_CURRENT_NETWORK:
{
const char *name (fActiveNetwork.FindString ("name"));
vision_app->RemoveNetwork (name);
BMenu *menu (fNetworkMenu->Menu ());
for (int32 i = 0; i < menu->CountItems (); i++)
{
BMenuItem *item (menu->ItemAt (i));
if (!strcmp (item->Label (), name))
{
delete menu->RemoveItem (i);
fActiveNetwork.MakeEmpty ();
dynamic_cast < BInvoker * >(menu->ItemAt (0))->Invoke ();
break;
}
}
}
break;
case M_DUPE_CURRENT_NETWORK:
{
if (msg->HasString ("text"))
{
fDupePrompt = NULL;
BString network (msg->FindString ("text"));
network.RemoveAll (" ");
BMenu *menu (fNetworkMenu->Menu ());
for (int32 i = 0; i < menu->CountItems (); i++)
{
BMenuItem *item (menu->ItemAt (i));
if (item && network == item->Label ())
{
dynamic_cast < BInvoker * >(item)->Invoke ();
return;
}
}
BMessage newNet = fActiveNetwork;
newNet.ReplaceString ("name", network.String ());
vision_app->SetNetwork (network.String (), &newNet);
BMenuItem *item (new BMenuItem (network.String (), new BMessage (M_CHOOSE_NETWORK)));
menu->AddItem (item, 0);
item->SetTarget (this);
dynamic_cast < BInvoker * >(item)->Invoke ();
}
else
{
BString promptText = B_TRANSLATE("Network Name");
promptText += ": ";
fDupePrompt = new PromptWindow (BPoint (Window ()->Frame ().left + Window ()->Frame ().Width () / 2, Window ()->Frame ().top + Window ()->Frame ().Height () / 2),
promptText.String(), B_TRANSLATE("Duplicate Current Network"), NULL, this, new BMessage (M_DUPE_CURRENT_NETWORK), NULL, false);
fDupePrompt->Show ();
}
}
break;
case M_SERVER_DATA_CHANGED:
{
UpdateNetworkData (fActiveNetwork);
}
break;
case M_SERVER_DIALOG:
{
BMessenger msgr (fServerPrefs);
if (msgr.IsValid ())
fServerPrefs->Activate ();
else
{
fServerPrefs = new NetPrefServerWindow (this);
fServerPrefs->SetNetworkData (&fActiveNetwork);
fServerPrefs->Show ();
}
}
break;
case M_NET_CHECK_LAG:
{
bool value = msg->FindInt32 ("be:value");
if (fActiveNetwork.HasBool ("lagCheck"))
fActiveNetwork.ReplaceBool ("lagCheck", value);
else
fActiveNetwork.AddBool ("lagCheck", value);
}
break;
case M_CONNECT_ON_STARTUP:
{
bool value = msg->FindInt32 ("be:value");
if (fActiveNetwork.HasBool ("connectOnStartup"))
fActiveNetwork.ReplaceBool ("connectOnStartup", value);
else
fActiveNetwork.AddBool ("connectOnStartup", value);
}
break;
case M_USE_NICK_DEFAULTS:
{
bool value = msg->FindInt32 ("be:value");
if (fActiveNetwork.HasBool ("useDefaults"))
fActiveNetwork.ReplaceBool ("useDefaults", value);
else
fActiveNetwork.AddBool ("useDefaults", value);
UpdatePersonalData (fActiveNetwork);
}
break;
case M_NETPREFS_TEXT_INVOKE:
{
if (fActiveNetwork.HasString("autoexec"))
fActiveNetwork.ReplaceString("autoexec", fTextView->Text());
else
fActiveNetwork.AddString("autoexec", fTextView->Text());
}
break;
case M_ADD_NICK:
if (msg->HasString ("text"))
{
fNickPrompt = NULL;
BString nick (msg->FindString ("text"));
nick.RemoveAll (" ");
for (int32 i = 0; i < fListView->CountItems (); i++)
{
BStringItem *item ((BStringItem *) fListView->ItemAt (i));
if (item && nick == item->Text ())
return;
}
fActiveNetwork.AddString ("nick", nick.String ());
fListView->AddItem (new BStringItem (nick.String ()));
}
else
{
BString promptString = B_TRANSLATE("Nickname");
promptString += ": ";
fNickPrompt = new PromptWindow (BPoint (Window ()->Frame ().left + Window ()->Frame ().Width () / 2, Window ()->Frame ().top + Window ()->Frame ().Height () / 2),
promptString.String(), B_TRANSLATE("Add Nickname"), NULL, this, new BMessage (M_ADD_NICK), NULL, false);
fNickPrompt->Show ();
}
break;
case M_REMOVE_NICK:
{
int32 current (fListView->CurrentSelection ());
if (current >= 0)
{
delete fListView->RemoveItem (current);
fActiveNetwork.RemoveData ("nick", current);
}
}
break;
case M_NICK_UP:
{
int32 current (fListView->CurrentSelection ());
BString nick1, nick2;
nick1 = fActiveNetwork.FindString ("nick", current);
nick2 = fActiveNetwork.FindString ("nick", current - 1);
fListView->SwapItems (current, current - 1);
fActiveNetwork.ReplaceString ("nick", current - 1, nick1.String ());
fActiveNetwork.ReplaceString ("nick", current, nick2.String ());
current = fListView->CurrentSelection ();
Window ()->DisableUpdates ();
fListView->DeselectAll ();
fListView->Select (current);
Window ()->EnableUpdates ();
}
break;
case M_NICK_DOWN:
{
int32 current (fListView->CurrentSelection ());
BString nick1, nick2;
nick1 = fActiveNetwork.FindString ("nick", current);
nick2 = fActiveNetwork.FindString ("nick", current + 1);
fListView->SwapItems (current, current + 1);
fActiveNetwork.ReplaceString ("nick", current + 1, nick1.String ());
fActiveNetwork.ReplaceString ("nick", current, nick2.String ());
current = fListView->CurrentSelection ();
Window ()->DisableUpdates ();
fListView->DeselectAll ();
fListView->Select (current);
Window ()->EnableUpdates ();
}
break;
case M_NICK_SELECTED:
{
int32 index (msg->FindInt32 ("index"));
if (index >= 0 && !fNickDefaultsBox->Value ())
{
fNickUpButton->SetEnabled (index > 0);
fNickDnButton->SetEnabled (index != (fListView->CountItems () - 1));
fNickRemoveButton->SetEnabled (true);
}
else
{
fNickUpButton->SetEnabled (false);
fNickDnButton->SetEnabled (false);
fNickRemoveButton->SetEnabled (false);
}
}
break;
default:
BView::MessageReceived (msg);
break;
}
}
long long SeqSummaryCommand::driverCreateSummary(map<int, long long>& startPosition, map<int, long long>& endPosition, map<int, long long>& seqLength, map<int, long long>& ambigBases, map<int, long long>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
try {
ofstream outSummary;
m->openOutputFile(sumFile, outSummary);
ifstream in;
m->openInputFile(filename, in);
in.seekg(filePos->start);
//print header if you are process 0
if (filePos->start == 0) {
outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
m->zapGremlins(in); m->gobble(in);
}
bool done = false;
int count = 0;
while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n"); }
Sequence current(in); m->gobble(in);
if (current.getName() != "") {
if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n"); }
int num = 1;
if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your name or count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
int thisStartPosition = current.getStartPos();
map<int, long long>::iterator it = startPosition.find(thisStartPosition);
if (it == startPosition.end()) { startPosition[thisStartPosition] = num; } //first finding of this start position, set count.
else { it->second += num; } //add counts
int thisEndPosition = current.getEndPos();
it = endPosition.find(thisEndPosition);
if (it == endPosition.end()) { endPosition[thisEndPosition] = num; } //first finding of this end position, set count.
else { it->second += num; } //add counts
int thisSeqLength = current.getNumBases();
it = seqLength.find(thisSeqLength);
if (it == seqLength.end()) { seqLength[thisSeqLength] = num; } //first finding of this length, set count.
else { it->second += num; } //add counts
int thisAmbig = current.getAmbigBases();
it = ambigBases.find(thisAmbig);
if (it == ambigBases.end()) { ambigBases[thisAmbig] = num; } //first finding of this ambig, set count.
else { it->second += num; } //add counts
int thisHomoP = current.getLongHomoPolymer();
it = longHomoPolymer.find(thisHomoP);
if (it == longHomoPolymer.end()) { longHomoPolymer[thisHomoP] = num; } //first finding of this homop, set count.
else { it->second += num; } //add counts
count++;
outSummary << current.getName() << '\t';
outSummary << thisStartPosition << '\t' << thisEndPosition << '\t';
outSummary << thisSeqLength << '\t' << thisAmbig << '\t';
outSummary << thisHomoP << '\t' << num << endl;
if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(num) + "\n"); }
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (in.eof()) { break; }
#endif
}
in.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
exit(1);
}
}
void ConfigParser::normalizeInput(
Json::Value& json,
const arbiter::Arbiter& arbiter)
{
Json::Value& input(json["input"]);
const bool verbose(json["verbose"].asBool());
const std::string extension(
input.isString() ?
arbiter::Arbiter::getExtension(input.asString()) : "");
const bool isInferencePath(extension == "entwine-inference");
if (!isInferencePath)
{
// The input source is a path or array of paths. First, we possibly
// need to expand out directories into their containing files.
FileInfoList fileInfo;
auto insert([&fileInfo, &arbiter, verbose](std::string in)
{
Paths current(arbiter.resolve(in, verbose));
for (const auto& c : current) fileInfo.emplace_back(c);
});
if (input.isArray())
{
for (const auto& entry : input)
{
if (entry.isString())
{
insert(directorify(entry.asString()));
}
else
{
fileInfo.emplace_back(entry);
}
}
}
else if (input.isString())
{
insert(directorify(input.asString()));
}
else return;
// Now, we have an array of files (no directories).
//
// Reset our input with our resolved paths. config.input.fileInfo will
// be an array of strings, containing only paths with no associated
// information.
input = Json::Value();
input.resize(fileInfo.size());
for (std::size_t i(0); i < fileInfo.size(); ++i)
{
input[Json::ArrayIndex(i)] = fileInfo[i].toJson();
}
}
else if (isInferencePath)
{
const std::string path(input.asString());
const Json::Value inference(parse(arbiter.get(path)));
input = inference["fileInfo"];
if (!json.isMember("schema")) json["schema"] = inference["schema"];
if (!json.isMember("bounds")) json["bounds"] = inference["bounds"];
if (!json.isMember("numPointsHint"))
{
json["numPointsHint"] = inference["numPoints"];
}
if (inference.isMember("reprojection"))
{
json["reprojection"] = inference["reprojection"];
}
if (Delta::existsIn(inference))
{
if (!json.isMember("scale")) json["scale"] = inference["scale"];
if (!json.isMember("offset")) json["offset"] = inference["offset"];
}
}
}
const bignum bignum::operator--(int)
{
bignum current(*this);
--(*this);
return move(current);
}
void push(const Transform& transform)
{
individual.push_back(transform);
Transform result = multiply(transform, current());
makeCurrent(result);
}
int main()
{
cout << "Hello, World!\n" ;
print_all(cout, "Hello", " World", '!', 0 ,'\n');
ui_history h(1);
current(h).emplace_back("Hello");
current(h).emplace_back("World");
current(h).emplace_back("1");
current(h).emplace_back("2");
current(h).emplace_back("3");
current(h).emplace_back("4");
current(h).emplace_back("5");
current(h).emplace_back("6");
current(h).emplace_back("7");
current(h).emplace_back("8");
current(h).emplace_back("9");
current(h).emplace_back("10");
current(h).emplace_back(my_class_t());
current(h).operator[](1).test();
current(h)[1].test();
ui_object uio = current(h)[1];
uio.test();
auto &uior = current(h)[1];
uior.test();
?? boost::uuids::uuid ot = uior.get_tag();
bool MainWindow::showSaveAsDialog()
{
if (!controller)
return false;
// Try current directory first
QFileInfo current(currentPath());
QString save_directory = current.canonicalPath();
if (save_directory.isEmpty())
{
// revert to least recently used directory or home directory.
QSettings settings;
save_directory = settings.value(QString::fromLatin1("openFileDirectory"), QDir::homePath()).toString();
}
// Build the list of supported file filters based on the file format registry
QString filters;
for (auto format : FileFormats.formats())
{
if (format->supportsExport())
{
if (filters.isEmpty())
filters = format->filter();
else
filters = filters + QLatin1String(";;") + format->filter();
}
}
QString filter; // will be set to the selected filter by QFileDialog
QString path = QFileDialog::getSaveFileName(this, tr("Save file"), save_directory, filters, &filter);
// On Windows, when the user enters "sample", we get "sample.omap *.xmap".
// (Fixed in upstream qtbase/src/plugins/platforms/windows/qwindowsdialoghelpers.cpp
// Wednesday March 20 2013 in commit 426f2cc.)
// This results in an error later, because "*" is not a valid character.
// But it is reasonable to apply the workaround to all platforms,
// due to the special meaning of "*" in shell patterns.
const int extensions_quirk = path.indexOf(QLatin1String(" *."));
if (extensions_quirk >= 0)
{
path.truncate(extensions_quirk);
}
if (path.isEmpty())
return false;
const FileFormat *format = FileFormats.findFormatByFilter(filter);
if (!format)
{
QMessageBox::information(this, tr("Error"),
tr("File could not be saved:") + QLatin1Char('\n') +
tr("There was a problem in determining the file format.") + QLatin1Char('\n') + QLatin1Char('\n') +
tr("Please report this as a bug.") );
return false;
}
// Ensure that the provided filename has a correct file extension.
// Among other things, this will ensure that FileFormats.formatForFilename()
// returns the same thing the user selected in the dialog.
// QString selected_extension = "." + format->primaryExtension();
QStringList selected_extensions(format->fileExtensions());
selected_extensions.replaceInStrings(QRegExp(QString::fromLatin1("^")), QString::fromLatin1("."));
bool has_extension = false;
for (auto selected_extension : qAsConst(selected_extensions))
{
if (path.endsWith(selected_extension, Qt::CaseInsensitive))
{
has_extension = true;
break;
}
}
if (!has_extension)
path += QLatin1Char('.') + format->primaryExtension();
// Ensure that the file name matches the format.
Q_ASSERT(format->fileExtensions().contains(QFileInfo(path).suffix()));
// Fails when using different formats for import and export:
// Q_ASSERT(FileFormats.findFormatForFilename(path) == format);
return savePath(path);
}
int FormWindowCursor::position() const
{
const int index = m_formWindow->widgets().indexOf(current());
return index == -1 ? 0 : index;
}
void PeptideBuilder::insert_(Residue& resnew, Residue& resold)
{
PDBAtom* pcarbon = getAtomByName_(resold, "C");
PDBAtom* pcarbona = getAtomByName_(resold, "CA");
PDBAtom* pnitrogen = getAtomByName_(resold, "N");
PDBAtom* pnitrogen_n = getAtomByName_(resnew, "N");
PDBAtom* pcarbona_n = getAtomByName_(resnew, "CA");
PDBAtom* pcarbon_n = getAtomByName_(resnew, "C");
Vector3 rot_axis; // axis for the torsion angle
// set C-N-bond
pcarbon->createBond(*pnitrogen_n)->setOrder(Bond::ORDER__SINGLE);;
// -------------- move N into 0|0|0
TranslationProcessor translation(Vector3(BOND_LENGTH_N_CA, 0., 0.));
resnew.apply(translation);
// --------------- calculate the coordinates for N
Vector3 CA_C_axis = (pcarbon->getPosition() - pcarbona->getPosition()).normalize();
Vector3 N_CA_axis = (pcarbona->getPosition() - pnitrogen->getPosition()).normalize();
Vector3 CA_N_axis = ((float)-1.) * N_CA_axis;
Vector3 newpos = (CA_N_axis - (CA_C_axis * CA_N_axis) * CA_C_axis).normalize();
Vector3 normaxis = (CA_C_axis % newpos).normalize();
Matrix4x4 mat;
mat.setRotation(Angle(-1. * 30.* Constants::PI/180.), normaxis);
newpos = mat * newpos; // rotation
newpos = newpos * BOND_LENGTH_N_C; // scaling of the bond length
newpos = newpos + pcarbon->getPosition();
// positioning of the nitrogen
translation.setTranslation(newpos);
resnew.apply(translation);
//---------------set the angle in NN to 120 degrees
Vector3 NN_C_axis = pcarbon->getPosition() - pnitrogen_n->getPosition();
Vector3 NN_NCA_axis = pcarbona_n->getPosition() - pnitrogen_n->getPosition();
CA_C_axis = pcarbon->getPosition() - pcarbona->getPosition();
// current angle for C
Angle current(acos(NN_C_axis * NN_NCA_axis /
(NN_C_axis.getLength() * NN_NCA_axis.getLength() )));
Matrix4x4 transmat;
Vector3 rotaxis;
if (current < (float)(Constants::PI - 1e-2))
{
current = Angle(120.*Constants::PI/180.) - current;
rotaxis = (NN_C_axis%NN_NCA_axis).normalize();
}
else
{
if (current > (float)(Constants::PI+1e-2))
{
// is this line really correct???
current = Angle(-120. * 120. * Constants::PI / 180.) - current;
rotaxis = (NN_C_axis % NN_NCA_axis).normalize();
}
else
{
current = Angle(-120. * Constants::PI / 180.) - current;
rotaxis = (NN_C_axis%CA_C_axis).normalize();
}
}
transmat.rotate(current, rotaxis);
TransformationProcessor transformation(transmat);
// translate to 0|0|0 (needed for the rotation)
Vector3 toOrigin = pnitrogen_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
// rotate in 0|0|0
resnew.apply(transformation);
// translate back to the correct position
translation.setTranslation(toOrigin);
resnew.apply(translation);
//---------------- set torsion angle to 0
Vector3 v_pca = pcarbona->getPosition();
Vector3 v_pc = pcarbon->getPosition();
Vector3 v_pn_n = pnitrogen_n->getPosition();
Vector3 v_pca_n = pcarbona_n->getPosition();
Vector3 v_pc_n = pcarbon_n->getPosition();
Vector3 v_pn =pnitrogen->getPosition();
current = getTorsionAngle( v_pca.x, v_pca.y, v_pca.z,
v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z );
rot_axis = (pnitrogen_n->getPosition() - pcarbon->getPosition()).normalize();
transmat.getZero();/// is this necessary???
transmat.rotate(Angle(-1. * current), rot_axis);
transformation.setTransformation(transmat);
// translate to 0|0|0
toOrigin = pnitrogen_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
// set torsion angles
resnew.apply(transformation);
// translate back
translation.setTranslation(toOrigin);
resnew.apply(translation);
// ---------------------set the peptide bond angle omega to 180 degrees
v_pca = pcarbona->getPosition();
v_pc = pcarbon->getPosition();
v_pn_n = pnitrogen_n->getPosition();
v_pca_n = pcarbona_n->getPosition();
v_pc_n = pcarbon_n->getPosition();
current = getTorsionAngle( v_pca.x, v_pca.y, v_pca.z,
v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z );
transmat.getZero();
transmat.rotate( Angle(Constants::PI , true),
(pnitrogen_n->getPosition() - pcarbon->getPosition()).normalize());
transformation.setTransformation(transmat);
// translate to 0|0|0 (needed for the rotation)
toOrigin = pnitrogen_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
//rotate in 0|0|0 about 180 degrees
resnew.apply(transformation);
//translate back
translation.setTranslation(toOrigin);
resnew.apply(translation);
//------------- angle psi
v_pca = pcarbona->getPosition();
v_pc = pcarbon->getPosition();
v_pn_n = pnitrogen_n->getPosition();
v_pca_n = pcarbona_n->getPosition();
v_pc_n = pcarbon_n->getPosition();
current = getTorsionAngle( v_pc.x, v_pc.y, v_pc.z,
v_pn_n.x, v_pn_n.y, v_pn_n.z,
v_pca_n.x, v_pca_n.y, v_pca_n.z,
v_pc_n.x, v_pc_n.y, v_pc_n.z );
rot_axis = (pcarbona_n->getPosition()-pnitrogen_n->getPosition()).normalize();
transmat.rotate(Angle(-1. * current), rot_axis);
transformation.setTransformation(transmat);
//translate to 0|0|0 (needed for the rotation)
toOrigin = pcarbona_n->getPosition();
translation.setTranslation(((float)(-1.))*toOrigin);
resnew.apply(translation);
resnew.apply(transformation);
// translate back to the correct position
translation.setTranslation(toOrigin);
resnew.apply(translation);
return;
}
void DialogTwaLine::traceIt()
{
line->deleteAll();
QListIterator<POI*> i (list);
while(i.hasNext())
{
POI * poi=i.next();
list.removeOne(poi);
if(poi->isPartOfTwa())
{
parent->slot_delPOI_list(poi);
delete poi;
}
}
this->myBoat=parent->getSelectedBoat();
if(myBoat==NULL) return;
if(!dataManager->isOk()) return;
if(!myBoat->getPolarData()) return;
time_t eta;
if(this->startGrib->isChecked() || myBoat->get_boatType()!=BOAT_VLM)
eta=dataManager->get_currentDate();
else
eta=((boatVLM*)myBoat)->getPrevVac()+myBoat->getVacLen();
nbVac[0]=this->spinBox->value();
nbVac[1]=this->spinBox_2->value();
nbVac[2]=this->spinBox_3->value();
nbVac[3]=this->spinBox_4->value();
nbVac[4]=this->spinBox_5->value();
twa[0]=this->doubleSpinBox->value();
twa[1]=this->doubleSpinBox_2->value();
twa[2]=this->doubleSpinBox_3->value();
twa[3]=this->doubleSpinBox_4->value();
twa[4]=this->doubleSpinBox_5->value();
mode[0]=this->TWA1->isChecked();
mode[1]=this->TWA2->isChecked();
mode[2]=this->TWA3->isChecked();
mode[3]=this->TWA4->isChecked();
mode[4]=this->TWA5->isChecked();
int vacLen=myBoat->getVacLen();
vlmPoint current(start.x(),start.y());
line->addVlmPoint(current);
double wind_speed,wind_angle,cap;
double lon=0,lat=0;
time_t maxDate=dataManager->get_maxDate();
bool crossing=false;
//int i1,j1,i2,j2;
GshhsReader *map=parent->get_gshhsReader();
int mapQuality=map?map->getQuality():4;
for (int page=0;page<5;page++)
{
if (nbVac[page]==0) continue;
for(int i=1;i<=nbVac[page];i++)
{
double current_speed=-1;
double current_angle=0;
if(!dataManager->getInterpolatedWind(current.lon, current.lat,
eta,&wind_speed,&wind_angle,INTERPOLATION_DEFAULT) || eta>maxDate)
break;
wind_angle=radToDeg(wind_angle);
if(dataManager->getInterpolatedCurrent(current.lon, current.lat,
eta,¤t_speed,¤t_angle,INTERPOLATION_DEFAULT))
{
current_angle=radToDeg(current_angle);
QPointF p=Util::calculateSumVect(wind_angle,wind_speed,current_angle,current_speed);
//qWarning()<<"cs="<<current_speed<<"cd="<<current_angle<<"tws="<<wind_speed<<"twd="<<wind_angle<<"Ltws="<<p.x()<<"Ltwd="<<p.y();
wind_speed=p.x();
wind_angle=p.y();
}
double TWA;
if(mode[page])
{
cap=A360(wind_angle+twa[page]);
TWA=twa[page];
}
else
{
cap=twa[page];
TWA=A360(cap-wind_angle);
if(qAbs(TWA)>180)
{
if(TWA<0)
TWA=360+TWA;
else
TWA=TWA-360;
}
}
double newSpeed=myBoat->getPolarData()->getSpeed(wind_speed,TWA);
if(current_speed>0)
{
QPointF p=Util::calculateSumVect(cap,newSpeed,A360(current_angle+180.0),current_speed);
newSpeed=p.x(); //in this case newSpeed is SOG
cap=p.y(); //in this case cap is COG
}
double distanceParcourue=newSpeed*vacLen/3600.00;
Util::getCoordFromDistanceAngle(current.lat, current.lon, distanceParcourue, cap,&lat,&lon);
if(!crossing && map && mapQuality>=3)
{
double I1,J1,I2,J2;
parent->getProj()->map2screenDouble(current.lon,current.lat,&I1,&J1);
parent->getProj()->map2screenDouble(lon,lat,&I2,&J2);
crossing=map->crossing(QLineF(I1,J1,I2,J2),QLineF(current.lon,current.lat,lon,lat));
}
current.lon=lon;
current.lat=lat;
line->addVlmPoint(current);
eta=eta+vacLen;
}
if(crossing)
pen.setColor(Qt::red);
else
pen.setColor(color);
line->setLinePen(pen);
QDateTime tm;
tm.setTimeSpec(Qt::UTC);
if(this->startVac->isChecked())
tm.setTime_t(eta-vacLen);
else
tm.setTime_t(eta);
//QString name;
//name.sprintf("Twa %.1f",twa[page]);
POI * arrival=parent->slot_addPOI(tr("ETA: ")+tm.toString("dd MMM-hh:mm"),0,lat,lon,-1,0,false,myBoat);
arrival->setPartOfTwa(true);
list.append(arrival);
}
line->slot_showMe();
QApplication::processEvents();
}
virtual void Execute(const DataObject &)
{
bool cardFound = false;
wxInt32 players = numPlayers();
wxInt32 curPlayer = current();
bool thisPlayerCard = false;
wxString thisPlayerName;
// Go through each player, starting with the current player. If
// they get a progress card, run the card dialog.
for(wxInt32 i = 0; i < players; ++i)
{
wxInt32 thisPlayer = (i + curPlayer) % players;
if(TRUE == playerGameData<wxInt32>(shGainProgressCard, thisPlayer))
{
// This player is now in a blocking action.
RULE.Execute(shRuleBeginBlockingAction, DataObject(thisPlayer));
// They have some.
cardFound = true;
// Shut everything down.
Controller::get().Transmit(shEventBuildUI,
DataObject(false, GetGame()));
Controller::get().Transmit(shEventControlsUI,
DataObject(false));
Controller::get().Transmit(shEventProgressCards,
DataObject(thisPlayer, GetGame()));
thisPlayerName = playerGame(thisPlayer).player().Name();
// See if this player is spending gold.
DataObject input(thisPlayer), output;
RULE.Decide(shLogicIsThisPlayer, input, output);
if(true == output.read<bool>())
{
thisPlayerCard = true;
}
// Only do this one at a time.
break;
}
}
// If all cards have been selected, continue on.
if(false == cardFound)
{
RULE.Execute(shRuleMarkerPostDiceRoll, DataObject());
}
// Otherwise, set the text.
else
{
wxString str1;
if(true == thisPlayerCard)
{
str1 = wxString::Format(stSelectAProgressCard.c_str(),
thisPlayerName.c_str());
}
else
{
str1 = wxString::Format(stWaitingSelectAProgressCard.c_str(),
thisPlayerName.c_str());
}
Controller::get().Transmit(shEventMessageUI, DataObject(str1,
GetGame()));
}
}
template<typename OutputType, typename RangeType, typename IlwOutput, typename IlwRange> std::string
RangeIterator<OutputType, RangeType, IlwOutput, IlwRange>::__str__(){
return "RangeIterator at value: " + std::to_string(current()) + " of Range: " + _rng->__str__();
}
void GlutWindow::mouseClick(int _button, int _state, int _x, int _y) {
current()->click(_button, _state, _x, _y);
}
