System* MolecularFileDialog::readMOL2File(String filename, String system_name)
{
setStatusbarText((String)tr("reading MOL2 file..."), true);
System* system = new System();
try
{
MOL2File mol2_file(filename);
mol2_file >> *system;
mol2_file.close();
}
catch(Exception::GeneralException& e)
{
setStatusbarText(tr("Reading of MOL2 file failed, see logs!"), true);
Log.error() << e << std::endl;
delete system;
return 0;
}
if (!finish_(filename, system_name, system)) return 0;
return system;
}
bool HelpViewer::showHelpFor(const QObject* object)
{
if (object == 0) return false;
HashMap<const QObject*, String>::Iterator to_find;
QObject* object2 = (QObject*) object;
QWidget* widget = dynamic_cast<QWidget*>(object2);
if (widget && widget->parent() != 0)
{
QToolBar* tb = dynamic_cast<QToolBar*>(widget->parent());
if (tb != 0)
{
QList<QAction *> acs = widget->actions();
if (acs.size() == 1)
{
to_find = docu_entries_.find(*acs.begin());
if (to_find != docu_entries_.end())
{
showHelp((*to_find).second);
return true;
}
}
}
}
while (object2 != 0)
{
to_find = docu_entries_.find(object2);
if (to_find != docu_entries_.end()) break;
object2 = object2->parent();
}
if (object2 == 0)
{
setStatusbarText(tr("No documentation for this widget available!"), true);
return false;
}
showHelp((*to_find).second);
return true;
}
bool MolecularFileDialog::writeXYZFile(String filename, const System& system)
{
try
{
XYZFile file(filename, std::ios::out);
file << system;
file.close();
}
catch(Exception::GeneralException& e)
{
Log.error() << e << std::endl;
setStatusbarText((String)tr("Writing of XYZ file failed, see logs!"), true);
return false;
}
return true;
}
/**
* Update the status bar if the package list view has loaded all
* package details.
*
* @param totalPackageCount The number of packages in the package list view.
*/
void PakooView::handleFinishedLoadingPackageInfo( int totalPackageCount )
{
QString category = packageView->listView->currentCategory();
QString subcategory = packageView->listView->currentSubcategory();
if( category == QString::null )
category = THEPORTAGETREETEXT;
else if( subcategory != QString::null )
category += "-" + subcategory;
emit showStatusbarProgress( false );
emit setStatusbarText(
PACKAGESINCATEGORYTEXT
.arg( totalPackageCount )
.arg( category )
.arg( packageView->listView->installedPackageCount() )
.arg( "" )
);
}
/**
* Update the status bar while the package list view is loading
* detailed package info.
*
* @param loadedPackageCount The number of packages loaded so far.
* @param totalPackageCount The total number of packages in the list view.
*/
void PakooView::handleLoadingPackageInfo( int loadedPackageCount,
int totalPackageCount )
{
QString category = packageView->listView->currentCategory();
QString subcategory = packageView->listView->currentSubcategory();
if( category == QString::null )
category = THEPORTAGETREETEXT;
else if( subcategory != QString::null )
category += "-" + subcategory;
emit setStatusbarProgress( loadedPackageCount, totalPackageCount, true );
emit setStatusbarText(
PACKAGESINCATEGORYTEXT
.arg( totalPackageCount )
.arg( category )
.arg( packageView->listView->installedPackageCount() )
.arg( LOADINGPACKAGEDETAILSTEXT )
);
}
void LabelDialog::accept()
{
list<Composite*> selection = getMainControl()->getMolecularControlSelection();
// no selection present => return
if (selection.empty()) return;
Representation* rep = new Representation;
rep->setProperty(Representation::PROPERTY__ALWAYS_FRONT);
rep->setModelType(MODEL_LABEL);
LabelModel* model = new LabelModel;
model->setText(ascii(text_box->currentText()));
model->setColor(custom_color_);
model->setFont(font_);
if ( all_items->isChecked()) model->setMode(LabelModel::ONE_LABEL);
else if ( every_atom->isChecked()) model->setMode(LabelModel::ALL_ATOMS);
else if (every_residue->isChecked()) model->setMode(LabelModel::ALL_RESIDUES);
else if ( every_item->isChecked()) model->setMode(LabelModel::ALL_ITEMS);
rep->setModelProcessor(model);
// process all objects in the selection list
list<Composite*>::const_iterator list_it = selection.begin();
list<const Composite*> composites;
for (; list_it != selection.end(); ++list_it)
{
composites.push_back(*list_it);
}
rep->setComposites(composites);
getMainControl()->insert(*rep);
getMainControl()->update(*rep);
text_box->addItem(text_box->currentText());
setStatusbarText(tr("Label added."));
}
void DownloadPDBFile::downloadFinished()
{
String id = ascii(pdbId->currentText());
String url = prefix_;
url += id;
url += (checkbox_biounit->isChecked()) ? biounit_suffix_ : suffix_;
Log.info() << "Url: " << url << std::endl;
if (current_reply_->error() != QNetworkReply::NoError)
{
Log.error() << "Could not download PDBFile! Reason given was \"" + (String)(current_reply_->errorString()) + "\""<< std::endl;
setStatusbarText("Could not download PDBFile! Reason given was \"" + (String)(current_reply_->errorString()) + "\"");
error_ = true;
}
else
{
System *system = new System();
try {
String temp_filename = VIEW::createTemporaryFilename();
QFile outfile(temp_filename.c_str());
outfile.open(QIODevice::ReadWrite);
outfile.write(current_reply_->readAll());
outfile.close();
// if we download the biological unit, we have to decompress the pdb.gz file
if (checkbox_biounit->isChecked())
{
String unzipped_filename = VIEW::createTemporaryFilename();
std::ifstream file(temp_filename.c_str(), std::ios_base::in | std::ios_base::binary);
boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
in.push(boost::iostreams::gzip_decompressor());
in.push(file);
PDBFile pdb_file(unzipped_filename, std::ios::out | std::ios::binary);
boost::iostreams::copy(in, pdb_file);
pdb_file.reopen(std::ios::in);
// the individual units are organized as MODELs
// by default PDBFile only reads the first MODEL
pdb_file.selectAllModels();
pdb_file >> *system;
pdb_file.close();
removeFile_(unzipped_filename);
}
else
{
PDBFile pdb_file(temp_filename);
pdb_file >> *system;
pdb_file.close();
}
removeFile_(temp_filename);
if (system->countAtoms() == 0)
{
delete system;
show();
setStatusbarText(tr("Could not fetch the given PDBFile"), true);
return;
}
else
{
setStatusbarText(String("read ") + String(system->countAtoms()) + " atoms for: " + id, true);
}
if (system->getName() == "")
{
system->setName(ascii(pdbId->currentText()));
}
system->setProperty("FROM_FILE", url);
close();
pdbId->clearEditText();
getMainControl()->insert(*system, ascii(pdbId->currentText()));
notify_(new CompositeMessage(*system, CompositeMessage::CENTER_CAMERA));
download->setDefault(true);
pdbId->setFocus();
}
catch(...)
bool MolecularFileDialog::writeFile()
{
list<Composite*>& selection = getMainControl()->getMolecularControlSelection();
if (selection.size() != 1 || !RTTI::isKindOf<System> (*selection.begin()))
{
setStatusbarText((String)tr("Not a single system selected! Aborting writing..."), true);
return false;
}
const System& system = *(const System*) (*selection.begin());
String file_name = getWorkingDir();
file_name += FileSystem::PATH_SEPARATOR;
file_name += system.getName();
file_name += ".pdb";
QString s = QFileDialog::getSaveFileName(
0,
tr("Choose a filename to save the selected system"),
file_name.c_str(),
getSupportedFileFormats().c_str());
if (s == QString::null) return false;
setStatusbarText((String)tr("writing file..."));
String filename = ascii(s);
setWorkingDirFromFilename_(filename);
String filter(filename);
while (filter.has(FileSystem::PATH_SEPARATOR))
{
filter = filter.after(FileSystem::PATH_SEPARATOR);
}
String filename_without_path = filter;
while (filter.has('.'))
{
filter = filter.after(".");
}
bool result = false;
if (filter == "PDB" || filter == "pdb" ||
filter == "ent" || filter == "ENT" ||
filter == "brk" || filter == "BRK")
{
result = writePDBFile(filename, system);
}
else if (filter.hasSubstring("HIN") || filter.hasSubstring("hin"))
{
result = writeHINFile(filename, system);
}
else if (filter.hasSubstring("MOL2") || filter.hasSubstring("mol2"))
{
result = writeMOL2File(filename, system);
}
else if (filter.hasSubstring("MOL") || filter.hasSubstring("mol"))
{
result = writeMOLFile(filename, system);
}
else if (filter.hasSubstring("SDF") || filter.hasSubstring("sdf"))
{
result = writeSDFile(filename, system);
}
else if (filter.hasSubstring("AC") || filter.hasSubstring("ac"))
{
result = writeACFile(filename, system);
}
else if (filter.hasSubstring("XYZ") || filter.hasSubstring("xyz"))
{
result = writeXYZFile(filename, system);
}
else
{
if (filter == filename_without_path)
{
filename += ".pdb";
result = writePDBFile(filename, system);
}
else
{
setStatusbarText((String)tr("Unknown file format, please set the file extension accordingly to type, aborting..."), true);
return false;
}
}
if (!result)
{
return false;
}
setStatusbarText(String(system.countAtoms()) + " " + (String)tr("atoms written to file") + " \"" + filename + "\"", true);
return true;
}
System* MolecularFileDialog::openMolecularFile(const String& filename,
const String& filetype,
const String& system_name)
{
bool ok = false;
try
{
if (File::isReadable(filename)) ok = true;
}
catch(...)
{}
if (!ok || filename == "/" || filename == "\\")
{
setStatusbarText((String)tr("Could not open file") + " " + filename, true);
return 0;
}
// TODO substitue by GenericMolFile* file = MolFileFactory::open(filename);
if (filetype.hasSubstring("pdb") || filetype.hasSubstring("PDB") ||
filetype.hasSubstring("brk") || filetype.hasSubstring("BRK") ||
filetype.hasSubstring("ent") || filetype.hasSubstring("ENT"))
{
return readPDBFile(filename, system_name);
}
else if (filetype.hasSubstring("HIN") ||
filetype.hasSubstring("hin"))
{
return readHINFile(filename, system_name);
}
else if (filetype.hasSubstring("MOL2") ||
filetype.hasSubstring("mol2"))
{
return readMOL2File(filename, system_name);
}
else if (filetype.hasSubstring("MOL") ||
filetype.hasSubstring("mol"))
{
return readMOLFile(filename, system_name);
}
else if (filetype.hasSubstring("SDF") ||
filetype.hasSubstring("sdf"))
{
return readSDFile(filename, system_name);
}
else if (filetype.hasSubstring("AC") ||
filetype.hasSubstring("ac"))
{
return readACFile(filename, system_name);
}
else if (filetype.hasSubstring("XYZ") ||
filetype.hasSubstring("xyz"))
{
return readXYZFile(filename, system_name);
}
else
{
setStatusbarText(String(tr("Unknown filetype")) + ": " + filetype, true);
}
return 0;
}
// creates a polygon from a given vector RegularData1D * data
void RegularData1DWidget::createPlot()
{
// no data => no polygon
if (data_ == 0 ||
data_->size() == 0)
{
return;
}
// find the data min and max
float min = (*data_)[0];
float max = (*data_)[0];
float dif_min = min;
float old = min; //last point
if (dif_min == 0) dif_min = 1;
for (int i=0; i<(int)data_->size(); i++)
{
if ((*data_)[i] >= max) max = (*data_)[i];
if ((*data_)[i] <= min) min = (*data_)[i];
float dif = (*data_)[i] - old;
if ( (dif > 1e-3) && (dif < dif_min) )
{
dif_min = dif;
}
old = (*data_)[i];
}
int height_ = (int)ceil(((max-min) / dif_min) * 5);
if (height_ > 1000)
{
// the resulting picture would be much too large
height_ = 1000;
dif_min = (max - min)/200.;
}
// resize the canvas to fit the data
canvas_.resize(5*(data_->size()+2), height_+10);
int x_new;
int y_new;
int x_old = 5;
int y_old = height_+5 - (int)((((*data_)[0]-min)/dif_min)*5);
Q3CanvasLine *ql;
try
{
for (int i=0; i<(int)data_->size(); i++)
{
x_new = 5*(i+1);
y_new = height_+5 - (int)(((data_->getData(i)-min)/dif_min)*5);
ql = new Q3CanvasLine(&canvas_);
ql->setPen(diagram_color_);
ql->show();
ql->setPoints(x_old, y_old, x_new, y_new);
objects_.push_back(dynamic_cast<Q3CanvasItem*> (ql));
x_old = x_new;
y_old = y_new;
}
}
catch(...)
{
setStatusbarText("Error: Point in dataset out of grid!");
Log.error() << "Error: Point in dataset out of grid!" << std::endl;
return;
}
//add the x-axis
ql = new Q3CanvasLine(&canvas_);
int startx = 1;
int starty = height_+5 - (int)/*round*/(((startx-min)/dif_min)*5);
int endx = data_->size()*5;
ql->setPoints(startx, starty, endx, starty);
ql->setPen(axis_color_);
ql->show();
objects_.push_back(dynamic_cast<Q3CanvasItem*> (ql));
//add the y-axis
ql = new Q3CanvasLine(&canvas_);
startx = 4;
starty = 0;
int endy = height_+5 - (int)/*round*/((((*data_)[endx]-min)/dif_min)*5);
ql->setPoints(startx, starty, startx, endy);
ql->setPen(QColor(Qt::red));
ql->show();
objects_.push_back(dynamic_cast<Q3CanvasItem*> (ql));
}
// creates a polygon from a given vector RegularData1D * data
void RegularData2DWidget::createPlot()
{
// no data => no polygon
if (data_ == 0 ||
data_->size() == 0)
{
return;
}
// set up the ColorMap... TODO: This should be done by a dialog or something similar
ColorRGBA colorList[3];
ColorMap color_table_;
colorList[0] = ColorRGBA(1.,0.,0.,1.);
colorList[1] = ColorRGBA(0.,1.,0.,1.);
colorList[2] = ColorRGBA(0.,0.,1.,1.);
color_table_.setBaseColors(colorList, 3);
color_table_.setNumberOfColors(100);
// determine the minimal and maximal values in data_
float min = (*data_)[0];
float max = (*data_)[0];
for (Position i=1; i < (*data_).size(); i++)
{
if ((*data_)[i] < min) min = (*data_)[i];
else if ((*data_)[i] > max) max = (*data_)[i];
}
color_table_.setRange(min, max);
color_table_.createMap();
//maximal number of Lines and Columns
Size max_x = (*data_).getSize().x;
Size max_y = (*data_).getSize().y;
// Draw the points
QPixmap pixmap;
pixmap.resize(max_x, max_y);
pixmap.fill(); // delete the old picture
QPainter paint;
paint.begin(&pixmap); // set the Painter
try
{
QColor pCol;
for (Position y=0; y< max_y; y++)
{
for (Position x=0; x< max_x; x++)
{
ColorRGBA mapcolor = color_table_.map(data_->getData(x + y * max_x));
pCol = QColor(mapcolor.getRed(), mapcolor.getGreen(), mapcolor.getBlue());
paint.setPen(pCol);
paint.drawPoint(x, y);
}
}
}
catch(...)
{
setStatusbarText("Error: Point in dataset out of grid!");
Log.error() << "Error: Point in dataset out of grid!" << std::endl;
return;
}
paint.end();
//put the pixmapItem into objects
PixmapItem* pixItem = new PixmapItem(&canvas_, pixmap);
pixItem->show();
objects_.push_back(dynamic_cast<Q3CanvasItem*> (pixItem));
// resize the canvas to fit the data
canvas_.resize(max_x, max_y);
}
