public static IChemModel readFromFileReader(final URL fileURL,
final String url, final String type,
final AbstractJChemPaintPanel panel) throws CDKException {
IChemModel chemModel = null;
WaitDialog.showDialog();
// InChI workaround - guessing for InChI results into an INChIReader
// (this does not work, we'd need an INChIPlainTextReader..)
// Instead here we use STDInChIReader, to be consistent throughout JCP
// using the nestedVm based classes.
try {
ISimpleChemObjectReader cor = null;
if (url.endsWith("txt")) {
// chemModel = StdInChIReader.readInChI(fileURL);
} else {
cor = FileHandler.createReader(fileURL, url, type);
chemModel = JChemPaint.getChemModelFromReader(cor, panel);
}
boolean avoidOverlap = true;
if (cor instanceof RGroupQueryReader) {
avoidOverlap = false;
}
JChemPaint.cleanUpChemModel(chemModel, avoidOverlap, panel);
} finally {
WaitDialog.hideDialog();
}
return chemModel;
}
/**
* Read an IChemModel from a given file.
*
* @param file
* @param type
* @param panel
* @return
* @throws CDKException
* @throws FileNotFoundException
*/
public static IChemModel readFromFile(final File file, final String type,
final AbstractJChemPaintPanel panel) throws CDKException,
FileNotFoundException {
final String url = file.toURI().toString();
ISimpleChemObjectReader cor = null;
try {
cor = FileHandler.createReader(file.toURI().toURL(), url, type);
} catch (final MalformedURLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (cor instanceof CMLReader) {
cor.setReader(new FileInputStream(file)); // hack
} else {
cor.setReader(new FileReader(file)); // hack
}
final IChemModel chemModel = JChemPaint.getChemModelFromReader(cor,
panel);
boolean avoidOverlap = true;
if (cor instanceof RGroupQueryReader) {
avoidOverlap = false;
}
JChemPaint.cleanUpChemModel(chemModel, avoidOverlap, panel);
return chemModel;
}