Hi,
I ran about the same kind of problem some weeks ago! The solution was that I
registered fristly some Reader to the factory and than I worked for me! Here is
a bit of the code! Hope this helps:
readerFactory = new ReaderFactory();
chemFormatList = new ArrayList<IChemFormatMatcher>();
if(readerFactory.getFormats().size() < 1) {
chemFormatList.add((IChemFormatMatcher)MDLFormat.getInstance());
chemFormatList.add((IChemFormatMatcher)MDLV2000Format.getInstance());
chemFormatList.add((IChemFormatMatcher)MDLV3000Format.getInstance());
chemFormatList.add((IChemFormatMatcher)SDFFormat.getInstance());
chemFormatList.add((IChemFormatMatcher)Mol2Format.getInstance());
chemFormatList.add((IChemFormatMatcher)CMLFormat.getInstance());
for (Iterator iter = chemFormatList.iterator();
iter.hasNext();) {
IChemFormatMatcher format =
(IChemFormatMatcher) iter.next();
readerFactory.registerFormat(format);
}
}
bufferedReader = new BufferedReader(new java.io.FileReader(fileName));
IChemObjectReader reader = readerFactory.createReader(bufferedReader);
Anywhy there is still the question if this is a feature or a bug of the cdk
that we firstly have to register that kind of readers before we want to use the
readerfactory. I would expect that the readerfactory knows defaultly the
readers supported by the cdk!
Cheers,
Thomas
> -----Ursprüngliche Nachricht-----
> Von: "sushil ronghe" <[EMAIL PROTECTED]>
> Gesendet: 11.04.07 13:29:12
> An: "Egon Willighagen" <[EMAIL PROTECTED]>
> CC: [email protected]
> Betreff: [Cdk-user] help
>
> I got the svn copy and successfully build the source in netbeans.
> Now i am running cdk with org.openscience.cdk.applications.FingerPrinter as a
> main class.
>
> i have provided the argument as "E:\Model\acetone.MOL"
>
> while running i got this error
>
> E:\Model\acetone.MOL: error=
> java.lang.NullPointerException
> at
> org.openscience.cdk.applications.FingerPrinter.main(FingerPrinter.java:76)
>
> then i checked the fingerPrinter.main class to see from where the error is
> coming
>
> it is coming from the highlighted area.
>
> Means the reader is null.
>
> IChemObjectReader reader = new ReaderFactory().createReader(new
> FileReader(input));
>
> why this is happening.
>
>
>
>
>
>
> try {
> File input = new File(ifilename);
>
> if(input.exists()){
> System.out.println("File is Alive");
> }
> if (!input.isDirectory()) {
>
> IChemObjectReader reader = new
> ReaderFactory().createReader(new FileReader(input));
> if (reader.accepts(Molecule.class)) {
> ChemFile content =
> (ChemFile)reader.read((ChemObject)new ChemFile());
>
> List containersList =
> ChemFileManipulator.getAllAtomContainers(content);
> if (containersList.size() > 0) {
> for (int j = 0; j < containersList.size
> (); j++) {
> String print =
> fingerprinter.getFingerprint((IAtomContainer)containersList.get(j)).toString();
> System.out.println(ifilename + " ("+ j +"):
> fingerprint=" + print);
>
> }
> }
> }
> }
> } catch (Exception exception) {}
>
>
>
> /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> strange,
>
> then i changed the code to
>
> Reader rr = new BufferedReader(new FileReader(input));
> IChemObjectReader reader = new ReaderFactory().createReader(rr);
>
>
>
> but all the way the reader is coming empty.I have checked the existance of
> file it is present.
>
> the same code is running well with the other jars.
>
>
>
> what could be the error and how can i solve it.
>
>
>
> please help..
>
>
>
>
>
> --
> ********************************
> sushil ronghe
> Center of Pharmacoinformatics
> India
> *********************************
>
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