void FolderWindow::SetStructures(int folderIndex)
{
StructureManager* structureManager = RNAStructViz::GetInstance()->GetStructureManager();
Folder* folder = structureManager->GetFolderAt(folderIndex);
m_folderIndex = folderIndex;
int shift = 0;
for( int ui = 0; ui < folder->structCount; ui++)
{
if(folder->folderStructs[(ui+shift)] == -1)
{
shift++;
}
int i = folder->folderStructs[(ui+shift)];
RNAStructure *strct = structureManager->GetStructure(i);
AddStructure(strct->GetFilename(), i);
}
label(folder->folderName);
char structLabel[MAX_BUFFER_SIZE];
snprintf(structLabel, MAX_BUFFER_SIZE - 1, " \n\n\n\n\n%s", folder->folderName);
ConfigParser::nullTerminateString(structLabel);
copy_label(structLabel);
labelsize(1.25 * LOCAL_TEXT_SIZE);
align(FL_ALIGN_TOP);
}
int InstallationObjectMenuComponent::handleObjectMenuSelect(SceneObject* sceneObject, CreatureObject* player, byte selectedID) {
if (!sceneObject->isInstallationObject())
return 1;
InstallationObject* installation = cast<InstallationObject*>(sceneObject);
ManagedReference<Zone*> zone = installation->getZone();
if (zone == NULL)
return 1;
if (!installation->isOnAdminList(player))
return 1;
StructureManager* structureManager = StructureManager::instance();
switch (selectedID) {
case 124:
player->executeObjectControllerAction(0x13F7E585, installation->getObjectID(), ""); //structureStatus
break;
case 129:
player->executeObjectControllerAction(0xE7E35B30, installation->getObjectID(), ""); //payMaintenance
break;
case 128:
player->executeObjectControllerAction(0x18FC1726, installation->getObjectID(), ""); //destroyStructure command
break;
case 131:
structureManager->promptMaintenanceDroid(installation,player);
break;
case 50:
structureManager->promptNameStructure(player, installation, installation);
//player->executeObjectControllerAction(0xC367B461, installation->getObjectID(), ""); //nameStructure
break;
case 51:
//TODO: Move to structure manager.
if (!installation->isGeneratorObject()) {
installation->handleStructureAddEnergy(player);
}
break;
case 121:
installation->sendPermissionListTo(player, "ADMIN");
break;
case 123:
installation->sendPermissionListTo(player, "HOPPER");
break;
default:
break;
}
return 0;
}
int PlaceStructureSessionImplementation::completeSession() {
if (constructionBarricade != NULL)
constructionBarricade->destroyObjectFromWorld(true);
String serverTemplatePath = deedObject->getGeneratedObjectTemplate();
StructureManager* structureManager = StructureManager::instance();
ManagedReference<StructureObject*> structureObject = structureManager->placeStructure(creatureObject, serverTemplatePath, positionX, positionY, directionAngle);
removeTemporaryNoBuildZone();
if (structureObject == NULL) {
ManagedReference<SceneObject*> inventory = creatureObject->getSlottedObject("inventory");
if (inventory != NULL)
inventory->transferObject(deedObject, -1, true);
return cancelSession();
}
structureObject->setDeedObjectID(deedObject->getObjectID());
deedObject->notifyStructurePlaced(creatureObject, structureObject);
ManagedReference<PlayerObject*> ghost = creatureObject->getPlayerObject();
if (ghost != NULL) {
ghost->addOwnedStructure(structureObject);
//Create Waypoint
ManagedReference<WaypointObject*> waypointObject = ( zone->getZoneServer()->createObject(String("object/waypoint/world_waypoint_blue.iff").hashCode(), 1)).castTo<WaypointObject*>();
waypointObject->setCustomObjectName(structureObject->getDisplayedName(), false);
waypointObject->setActive(true);
waypointObject->setPosition(positionX, 0, positionY);
waypointObject->setPlanetCRC(zone->getZoneCRC());
ghost->addWaypoint(waypointObject, false, true);
//Create an email.
ManagedReference<ChatManager*> chatManager = zone->getZoneServer()->getChatManager();
if (chatManager != NULL) {
UnicodeString subject = "@player_structure:construction_complete_subject";
StringIdChatParameter emailBody("@player_structure:construction_complete");
emailBody.setTO(structureObject->getObjectName());
emailBody.setDI(ghost->getLotsRemaining());
chatManager->sendMail("@player_structure:construction_complete_sender", subject, emailBody, creatureObject->getFirstName(), waypointObject);
}
if (structureObject->isBuildingObject() && !structureObject->isGCWBase()) {
BuildingObject* building = cast<BuildingObject*>(structureObject.get());
building->setCustomObjectName(creatureObject->getFirstName() + "'s House", true); //Set the house sign.
}
}
return cancelSession(); //Canceling the session just removes the session from the player's map.
}
void CityRegionImplementation::destroyAllStructuresForRank(uint8 rank, bool sendMail) {
Locker locker(_this.getReferenceUnsafeStaticCast());
if (zone == NULL)
return;
StructureManager* structureManager = StructureManager::instance();
for (int i = structures.size() - 1; i >= 0; --i) {
ManagedReference<StructureObject*> structure = structures.get(i);
SharedStructureObjectTemplate* ssot = dynamic_cast<SharedStructureObjectTemplate*>(structure->getObjectTemplate());
//We only want to destroy civic structures.
if (ssot == NULL || ssot->getCityRankRequired() < rank || !ssot->isCivicStructure())
continue;
sendDestroyObjectMail(structure);
Locker _clocker(structure, _this.getReferenceUnsafeStaticCast());
structureManager->destroyStructure(structure);
structures.removeElement(structure);
}
for (int i = cityDecorations.size() - 1; i >= 0; --i) {
ManagedReference<SceneObject*> decoration = cityDecorations.get(i);
StructureObject* structure = decoration.castTo<StructureObject*>();
if (structure == NULL)
continue;
SharedStructureObjectTemplate* ssot = dynamic_cast<SharedStructureObjectTemplate*>(structure->getObjectTemplate());
//We only want to destroy civic structures.
if (ssot == NULL || ssot->getCityRankRequired() < rank || !ssot->isCivicStructure())
continue;
sendDestroyObjectMail(structure);
Locker _clocker(structure, _this.getReferenceUnsafeStaticCast());
structureManager->destroyStructure(structure);
cityDecorations.removeElement(decoration);
}
}
void FolderWindow::SetStructures(int folderIndex)
{
StructureManager* structureManager = RNAStructViz::GetInstance()->GetStructureManager();
Folder* folder = structureManager->GetFolderAt(folderIndex);
m_folderIndex = folderIndex;
int shift = 0;
for( int ui = 0; ui < folder->structCount; ui++)
{
if(folder->folderStructs[(ui+shift)] == -1)
{
shift++;
}
int i = folder->folderStructs[(ui+shift)];
RNAStructure *strct = structureManager->GetStructure(i);
AddStructure(strct->GetFilename(), i);
}
this->label(folder->folderName);
/*sprintf(title, "Folder: %-.48s", structureManager->GetFolderAt(folderIndex)->folderName);
label(title);*/
}
void ZoneServerImplementation::startZones() {
info("Loading zones.");
SortedVector<String>* enabledZones = configManager->getEnabledZones();
StructureManager* structureManager = StructureManager::instance();
structureManager->setZoneServer(_this.getReferenceUnsafeStaticCast());
for (int i = 0; i < enabledZones->size(); ++i) {
String zoneName = enabledZones->get(i);
info("Loading zone " + zoneName + ".");
Zone* zone = new Zone(processor, zoneName);
zone->createContainerComponent();
zone->initializePrivateData();
zone->deploy("Zone " + zoneName);
zones->put(zoneName, zone);
}
resourceManager->initialize();
for (int i = 0; i < zones->size(); ++i) {
Zone* zone = zones->get(i);
if (zone != NULL) {
ZoneLoadManagersTask* task = new ZoneLoadManagersTask(_this.getReferenceUnsafeStaticCast(), zone);
task->execute();
}
}
for (int i = 0; i < zones->size(); ++i) {
Zone* zone = zones->get(i);
if (zone != NULL) {
while (!zone->hasManagersStarted())
Thread::sleep(500);
}
}
}
/*May not be quite right, modified from orignial code*/
void StatsWindow::ClearTruthValues()
{
StructureManager* structureManager = RNAStructViz::GetInstance()->GetStructureManager();
Folder* folder = structureManager->GetFolderAt(folderIndex);
int shift = 0;
for(int i = 0; i < folder->structCount; i++)
{
if(folder->folderStructs[(i + shift)] == -1)
shift++;
if(folder->folderStructs[(i + shift)] != -1)
{
RNAStructure *structure = structureManager->GetStructure((i+shift));
if(!structure)
continue;
int length = structure->GetLength();
for (int j = 0; j < length; ++j)
{
structure->GetBaseAt(j)->m_truth = RNAStructure::TruePositive;
}
}
}
}
void DiagramWindow::draw()
{
Fl_Color priorColor = fl_color();
int priorFont = fl_font();
int priorFontSize = fl_size();
fl_color(color());
fl_rectf(0, 0, w(), h());
fl_color(priorColor);
Fl_Window::draw();
// Get the structures. Be sure the reference structure is first.
RNAStructure* sequences[3];
StructureManager* structureManager = RNAStructViz::GetInstance()->GetStructureManager();
for (int j = 0; j < 3; ++j)
{
if ((int)(m_menuItems[m_menus[j]->value()].user_data()) == -1)
{
sequences[j] = 0;
}
else
{
sequences[j] = structureManager->GetStructure((int)(m_menuItems[m_menus[j]->value()].user_data()));
}
}
int numToDraw = 0;
if (sequences[0])
{
if (sequences[1])
{
if (sequences[2])
{
numToDraw = 3;
DrawKey3();
}
else
{
numToDraw = 2;
DrawKey2(0, 1);
}
}
else
{
if (sequences[2])
{
sequences[1] = sequences[2];
DrawKey2(0, 2);
numToDraw = 2;
}
else
{
DrawKey1(0);
numToDraw = 1;
}
}
}
else
{
if (sequences[1])
{
if (sequences[2])
{
sequences[0] = sequences[1];
sequences[1] = sequences[2];
DrawKey2(1, 2);
numToDraw = 2;
}
else
{
sequences[0] = sequences[1];
DrawKey1(1);
numToDraw = 1;
}
}
else
{
if (sequences[2])
{
sequences[0] = sequences[2];
DrawKey1(2);
numToDraw = 1;
}
else
{
numToDraw = 0;
}
}
}
if (m_redrawStructures)
{
{
fl_begin_offscreen(m_offscreenImage[0]);
RedrawBuffer(sequences, numToDraw, 2048);
fl_read_image(m_imageData[0], 0, 0, 2048, 2048);
fl_end_offscreen();
}
{
fl_begin_offscreen(m_offscreenImage[1]);
RedrawBuffer(sequences, numToDraw, 1024);
fl_read_image(m_imageData[1], 0, 0, 1024, 1024);
fl_end_offscreen();
}
m_glWindow->UpdateTexture();
m_redrawStructures = false;
}
m_glWindow->redraw();
fl_color(priorColor);
fl_font(priorFont, priorFontSize);
fl_line_style(0);
}
void DiagramWindow::RebuildMenus()
{
// Create the menus, if they don't already exist.
int activeMenuIndex[3];
bool activeSet[3];
if (!m_menus[0])
{
this->begin();
Fl_Box* label = new Fl_Box(ms_menu_minx[0], 0, ms_menu_width, 25, "Structure 1");
label->labelcolor(FL_WHITE);
label = new Fl_Box(ms_menu_minx[1], 0, ms_menu_width, 25, "Structure 2");
label->labelcolor(FL_WHITE);
label = new Fl_Box(ms_menu_minx[2], 0, ms_menu_width, 25, "Structure 3");
label->labelcolor(FL_WHITE);
m_menus[0] = new Fl_Choice(ms_menu_minx[0], 25, ms_menu_width, 25);
m_menus[1] = new Fl_Choice(ms_menu_minx[1], 25, ms_menu_width, 25);
m_menus[2] = new Fl_Choice(ms_menu_minx[2], 25, ms_menu_width, 25);
m_menus[0]->callback(MenuCallback);
m_menus[1]->callback(MenuCallback);
m_menus[2]->callback(MenuCallback);
activeMenuIndex[0] = -1;
activeMenuIndex[1] = -1;
activeMenuIndex[2] = -1;
activeSet[0] = false;
activeSet[1] = false;
activeSet[2] = false;
this->end();
}
else
{
// Cache the current active index, if any
for (int j = 0; j < 3; ++j)
{
activeMenuIndex[j] = (int)m_menus[j]->mvalue()->user_data();
activeSet[j] = false;
}
}
// Remove any unnecessary menu items
for (int i = m_structures.size() + 1; i < m_menuItemsSize; ++i)
{
m_menuItems[i].label(0);
}
// Reallocate if necessary
if ((int)m_structures.size() + 2 > m_menuItemsSize)
{
m_menuItemsSize = m_structures.size() + 2;
free(m_menuItems);
m_menuItems = (Fl_Menu_Item*)malloc(sizeof(Fl_Menu_Item) * m_menuItemsSize);
m_menuItems[0].label("None");
m_menuItems[0].shortcut(0);
m_menuItems[0].user_data((void*)-1);
for (int i = 0; i < m_menuItemsSize; ++i)
{
m_menuItems[i].callback((Fl_Callback*)0);
m_menuItems[i].labeltype(FL_NORMAL_LABEL);
m_menuItems[i].labelsize(m_menus[0]->textsize());
m_menuItems[i].labelcolor(FL_BLACK);
m_menuItems[i].labelfont(m_menus[0]->textfont());
m_menuItems[i].flags = 0;
}
m_menus[0]->menu(m_menuItems);
m_menus[1]->menu(m_menuItems);
m_menus[2]->menu(m_menuItems);
}
// Add entries
StructureManager* structureManager = RNAStructViz::GetInstance()->GetStructureManager();
for (unsigned int ui = 0; ui < m_structures.size(); ++ui)
{
RNAStructure* structure = structureManager->GetStructure(m_structures[ui]);
m_menuItems[ui + 1].label(structure->GetFilename());
m_menuItems[ui + 1].user_data((void*)m_structures[ui]);
m_menuItems[ui + 1].shortcut(0);
for (int j = 0; j < 3; ++j)
{
if (activeMenuIndex[j] == m_structures[ui])
{
m_menus[j]->value(ui + 1);
activeSet[j] = true;
}
}
}
// Reset active entries that have not already been set, and set the last entry to NULL label
m_menuItems[m_structures.size() + 1].label(0);
for (int j = 0; j < 3; ++j)
{
if (!activeSet[j])
{
m_menus[j]->value(m_menuItems);
}
}
}
/*May not be quite right, modified from orignial code*/
void StatsWindow::UpdateTruthValues()
{
if (referenceIndex == -1)
{
ClearTruthValues();
return;
}
StructureManager* structureManager = RNAStructViz::GetInstance()->GetStructureManager();
Folder* folder = structureManager->GetFolderAt(folderIndex);
RNAStructure* refStructure = structureManager->GetStructure(referenceIndex);
int length = refStructure->GetLength();
for (int j = 0; j < length; ++j)
{
refStructure->GetBaseAt(j)->m_truth = RNAStructure::TruePositive;
}
int shift = 0;
for (int i = 0; i < folder->structCount; ++i)
{
if(folder->folderStructs[(i + shift)] == -1)
shift++;
if(folder->folderStructs[(i + shift)] != -1)
{
RNAStructure* otherStructure = structureManager->GetStructure((i+shift));
if (!otherStructure || otherStructure == refStructure)
continue;
for (int j = 0; j < length; ++j)
{
RNAStructure::BaseData* refBase = refStructure->GetBaseAt(j);
RNAStructure::BaseData* otherBase = otherStructure->GetBaseAt(j);
if (refBase->m_pair == RNAStructure::UNPAIRED)
{
if (otherBase->m_pair == RNAStructure::UNPAIRED)
{
otherBase->m_truth = RNAStructure::TrueNegative;
}
else
{
otherBase->m_truth = RNAStructure::FalsePositive;
}
}
else
{
if (otherBase->m_pair == RNAStructure::UNPAIRED)
{
otherBase->m_truth = RNAStructure::FalseNegative;
}
else if (otherBase->m_pair == refBase->m_pair)
{
otherBase->m_truth = RNAStructure::TruePositive;
}
else
{
otherBase->m_truth = RNAStructure::FalsePositive;
}
}
}
}
}
}
void DrawingWindow::draw()
{
Fl_Double_Window::draw();
if (m_activeIndices.empty())
return;
// Get the structures. Be sure the reference structure is first.
RNAStructure** sequences = (RNAStructure**)malloc(sizeof(RNAStructure*) * m_activeIndices.size());
StructureManager* structureManager = RNAStructViz::GetStructureManager();
int posn = 0;
for (unsigned int i = 0; i < m_activeIndices.size(); ++i)
{
if (m_activeIndices[i] == structureManager->GetReferenceStructure())
{
sequences[posn++] = structureManager->GetStructure(m_activeIndices[i]);
}
}
for (unsigned int i = 0; i < m_activeIndices.size(); ++i)
{
if (m_activeIndices[i] != structureManager->GetReferenceStructure())
{
sequences[posn++] = structureManager->GetStructure(m_activeIndices[i]);
}
}
fl_color(FL_BLACK);
// Draw the circle of bases
int numBases = sequences[0]->GetLength();
float angleDelta = (M_PI * 2.0f - 0.2f) / (float)numBases;
float centerX = (float)w() / 2.0f;
float centerY = (float)h() / 2.0f;
float radius = centerX < centerY ? centerX - 20.f : centerY - 20.f;
float angle = 1.5f * M_PI - 0.1f;
for (int i = 0; i < numBases; ++i)
{
float xPosn = centerX + cos(angle) * radius;
float yPosn = centerY - sin(angle) * radius;
switch (sequences[0]->GetBaseAt(i)->m_base)
{
case RNAStructure::A:
fl_draw("A", xPosn, yPosn);
break;
case RNAStructure::C:
fl_draw("C", xPosn, yPosn);
break;
case RNAStructure::G:
fl_draw("G", xPosn, yPosn);
break;
case RNAStructure::U:
fl_draw("U", xPosn, yPosn);
break;
}
angle -= angleDelta;
fl_point((int)xPosn, (int)yPosn);
}
// Clean up
free(sequences);
}
InputWindow::InputWindow(int w, int h, const char *label,
const char *defaultName, InputWindowType type, int folderIndex) :
Fl_Window(MAX(w, 445), h, label), cbUseDefaultNames(NULL), ctFileChooser(NULL),
userWindowStatus(OK), fileSelectionIndex(-1)
{
string = (char*)malloc(sizeof(char)*90);
color(GUI_WINDOW_BGCOLOR);
set_modal();
windowType = type;
inputText = (char *) malloc(MAX_BUFFER_SIZE * sizeof(char));
if(type == InputWindow::FILE_INPUT) {
strncpy(inputText, defaultName, MAX_BUFFER_SIZE - 1);
inputText[MAX_BUFFER_SIZE - 1] = '\0';
char *extPtr = strrchr(inputText, '.');
if(extPtr != NULL) {
*extPtr = '\0';
}
char *filenameStartPtr = strrchr(inputText, '/');
int fnameStartPos;
if(filenameStartPtr != NULL) {
fnameStartPos = filenameStartPtr - inputText;
}
else {
fnameStartPos = 0;
}
char saveDirInfo[MAX_BUFFER_SIZE];
snprintf(saveDirInfo, fnameStartPos + 1, "%s", inputText);
sprintf(string, "Export to Directory: %s", saveDirInfo);
input = new Fl_Input(25, 50, 235, 30);
input->when(FL_WHEN_ENTER_KEY);
input->value(filenameStartPtr + 1);
Fl_Box *box = new Fl_Box(110, 20, 100, 30, (const char*)string);
box->box(FL_NO_BOX);
box->align(FL_ALIGN_CENTER);
Fl_Box *fileExtBox = new Fl_Box(260,50,30,30,".csv");
Fl_Button *button = new Fl_Button(305, 50, 110, 30, "Export to CSV @->");
button->callback(InputCallback, (void*)0);
button->set_active();
input->callback(InputCallback, (void*)0);
callback(CloseCallback);
}
else if(type == InputWindow::FOLDER_INPUT) {
std::string actualStructName =
ExtractStructureNameFromCTName(defaultName);
const char *actualStructNameCStr = actualStructName.c_str();
strncpy(inputText, actualStructNameCStr, actualStructName.size() + 1);
ConfigParser::nullTerminateString(inputText, actualStructName.size());
sprintf(string, "Creating new folder for the CT structure %s", defaultName);
input = new Fl_Input(160, 50, 250, 30, "@fileopen New Folder Name:");
input->when(FL_WHEN_ENTER_KEY);
input->maximum_size(60);
input->value(inputText);
input->color(GUI_BGCOLOR);
input->textcolor(GUI_BTEXT_COLOR);
Fl_Box *box = new Fl_Box(50, 1, 350, 40, (const char*) string);
box->box(FL_OSHADOW_BOX);
box->align(FL_ALIGN_CENTER | FL_ALIGN_INSIDE | FL_ALIGN_WRAP);
box->color(GUI_BGCOLOR);
box->labelcolor(GUI_BTEXT_COLOR);
Fl_Button *button = new Fl_Button(340, 50, 100, 30, "Add Folder @|>");
button->callback(InputCallback, (void*)0);
button->labelcolor(GUI_BTEXT_COLOR);
button->set_active();
input->callback(InputCallback, (void*)0);
input->labelcolor(GUI_TEXT_COLOR);
const char *cbText = " Use only default names for structure folders";
cbUseDefaultNames = new Fl_Check_Button(30, 100, 375, 30, cbText);
cbUseDefaultNames->box(FL_ROUND_UP_BOX);
cbUseDefaultNames->color(GUI_BGCOLOR);
cbUseDefaultNames->labelcolor(GUI_BTEXT_COLOR);
cbUseDefaultNames->down_color(GUI_WINDOW_BGCOLOR);
cbUseDefaultNames->align(FL_ALIGN_LEFT | FL_ALIGN_INSIDE | FL_ALIGN_CENTER);
callback(CloseCallback);
}
else {
const char *windowDisplayMsg = "Which CT file structure for the organism\ndo you want to display?";
Fl_Box *box = new Fl_Box(75, 5, 300, 40, windowDisplayMsg);
box->box(FL_RSHADOW_BOX);
box->align(FL_ALIGN_CENTER | FL_ALIGN_INSIDE | FL_ALIGN_WRAP);
box->color(GUI_BGCOLOR);
box->labelcolor(GUI_BTEXT_COLOR);
Fl_Button *displayButton = new Fl_Button(100, 100, 200, 30, "Display Zoomed Region @|>");
displayButton->callback(DisplayCTFileCallback, (void*)0);
displayButton->color(GUI_BGCOLOR);
displayButton->labelcolor(GUI_BTEXT_COLOR);
displayButton->set_active();
//displayButton->shortcut(FL_Enter);
Fl_Button *cancelButton = new Fl_Button(310, 100, 75, 30, "Cancel @1+");
cancelButton->callback(CancelCallback);
cancelButton->color(GUI_BGCOLOR);
cancelButton->labelcolor(GUI_BTEXT_COLOR);
ctFileChooser = new Fl_Choice(175, 55, 215, 30, "Choose CT Structure: ");
ctFileChooser->color(GUI_BGCOLOR);
ctFileChooser->labelcolor(GUI_BTEXT_COLOR);
StructureManager *structManager = RNAStructViz::GetInstance()->GetStructureManager();
Folder *curFolder = structManager->GetFolderAt(folderIndex);
for(int s = 0; s < curFolder->structCount; s++) {
RNAStructure *rnaStruct = structManager->GetStructure(curFolder->folderStructs[s]);
const char *ctFileName = rnaStruct->GetFilename();
ctFileChooser->add(ctFileName);
}
ctFileChooser->value(0);
}
show();
if(type != InputWindow::FOLDER_INPUT || !GUI_USE_DEFAULT_FOLDER_NAMES) {
show();
}
else {
show();
InputCallback((Fl_Widget *) cbUseDefaultNames, (void *) NULL);
}
}
