public static void showInstance(final File inFile, final String type,
final AbstractJChemPaintPanel jcpPanel, final boolean debug) {
try {
final IChemModel chemModel = JChemPaint.readFromFile(inFile, type,
jcpPanel);
final String name = inFile.getName();
final JChemPaintPanel p = JChemPaint.showInstance(chemModel, name,
debug);
p.setCurrentWorkDirectory(inFile.getParentFile());
p.setLastOpenedFile(inFile);
p.setIsAlreadyAFile(inFile);
} catch (final CDKException ex) {
JOptionPane.showMessageDialog(jcpPanel, ex.getMessage());
return;
} catch (final FileNotFoundException e) {
JOptionPane.showMessageDialog(jcpPanel, GT._("File does not exist")
+ ": " + inFile.getPath());
return;
}
}
public static JChemPaintPanel showInstance(final IChemModel chemModel,
final String title, final boolean debug) {
final JFrame f = new JFrame(title + " - JChemPaint");
chemModel.setID(title);
f.addWindowListener(new JChemPaintPanel.AppCloser());
f.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
final JChemPaintPanel p = new JChemPaintPanel(chemModel,
GUI_APPLICATION, debug, null, new ArrayList<String>());
p.updateStatusBar();
f.setPreferredSize(new Dimension(800, 494)); // 1.618
f.add(p);
f.pack();
final Point point = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getCenterPoint();
final int w2 = f.getWidth() / 2;
final int h2 = f.getHeight() / 2;
f.setLocation(point.x - w2, point.y - h2);
f.setVisible(true);
frameList.add(f);
return p;
}
/**
* Returns an IChemModel, using the reader provided (picked).
*
* @param cor
* @param panel
* @return
* @throws CDKException
*/
public static IChemModel getChemModelFromReader(
final ISimpleChemObjectReader cor,
final AbstractJChemPaintPanel panel) throws CDKException {
panel.get2DHub().setRGroupHandler(null);
String error = null;
ChemModel chemModel = null;
IChemFile chemFile = null;
if (cor.accepts(IChemFile.class) && chemModel == null) {
// try to read a ChemFile
try {
chemFile = (IChemFile) cor.read((IChemObject) new ChemFile());
if (chemFile == null) {
error = "The object chemFile was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: " + exception.getMessage();
exception.printStackTrace();
}
}
if (error != null) {
throw new CDKException(error);
}
if (chemModel == null && chemFile != null) {
chemModel = (ChemModel) chemFile.getChemSequence(0).getChemModel(0);
}
if (cor.accepts(ChemModel.class) && chemModel == null) {
// try to read a ChemModel
try {
chemModel = (ChemModel) cor.read((IChemObject) new ChemModel());
if (chemModel == null) {
error = "The object chemModel was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: " + exception.getMessage();
exception.printStackTrace();
}
}
// Smiles reading
if (cor.accepts(AtomContainerSet.class) && chemModel == null) {
// try to read a AtomContainer set
try {
final IAtomContainerSet som = cor.read(new AtomContainerSet());
chemModel = new ChemModel();
chemModel.setMoleculeSet(som);
if (chemModel == null) {
error = "The object chemModel was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: " + exception.getMessage();
exception.printStackTrace();
}
}
// MDLV3000 reading
if (cor.accepts(AtomContainer.class) && chemModel == null) {
// try to read a AtomContainer
final IAtomContainer mol = cor.read(new AtomContainer());
if (mol != null) {
try {
final IAtomContainerSet newSet = new AtomContainerSet();
newSet.addAtomContainer(mol);
chemModel = new ChemModel();
chemModel.setMoleculeSet(newSet);
if (chemModel == null) {
error = "The object chemModel was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: "
+ exception.getMessage();
exception.printStackTrace();
}
}
}
// RGroupQuery reading
if (cor.accepts(RGroupQuery.class) && chemModel == null) {
final IRGroupQuery rgroupQuery = cor.read(new RGroupQuery());
if (rgroupQuery != null) {
try {
chemModel = new ChemModel();
final RGroupHandler rgHandler = new RGroupHandler(
rgroupQuery);
panel.get2DHub().setRGroupHandler(rgHandler);
chemModel.setMoleculeSet(rgHandler
.getMoleculeSet(chemModel));
rgHandler.layoutRgroup();
} catch (final Exception exception) {
error = "Error while reading file: "
+ exception.getMessage();
exception.printStackTrace();
}
}
}
if (error != null) {
throw new CDKException(error);
}
if (chemModel == null && chemFile != null) {
chemModel = (ChemModel) chemFile.getChemSequence(0).getChemModel(0);
}
// SmilesParser sets valencies, switch off by default.
if (cor instanceof SMILESReader) {
final IAtomContainer allinone = JChemPaintPanel
.getAllAtomContainersInOne(chemModel);
for (int k = 0; k < allinone.getAtomCount(); k++) {
allinone.getAtom(k).setValency(null);
}
}
return chemModel;
}