Examples with ICiteable ambit2.base.interfaces.ICiteable used on opensource projects

Example 1 with ICiteable

use of ambit2.base.interfaces.ICiteable in project ambit-mirror by ideaconsult.

the class RawIteratingFolderReader method getItemReader.

protected IRawReader<IStructureRecord> getItemReader(int index) throws Exception {
    String name = files[index].getName().toLowerCase();
    if (name.endsWith(FileInputState._FILE_TYPE.SDF_INDEX.getExtension())) {
        RawIteratingSDFReader r = new RawIteratingSDFReader(new FileReader(files[index]));
        r.setReference(LiteratureEntry.getInstance(files[index].getName(), "file:///" + files[index].getAbsolutePath()));
        return (IRawReader<IStructureRecord>) r;
    } else if (name.endsWith(FileInputState._FILE_TYPE.MOL_INDEX.getExtension())) {
        RawIteratingMOLReader r = new RawIteratingMOLReader(new FileReader(files[index]));
        r.setReference(LiteratureEntry.getInstance(files[index].getName(), "file:///" + files[index].getAbsolutePath()));
        return (IRawReader<IStructureRecord>) r;
    } else if (name.endsWith(FileInputState._FILE_TYPE.I5D_INDEX.getExtension())) {
        IIteratingChemObjectReader r = FileInputState.getI5DReader(files[index]);
        if (r instanceof ICiteable) {
            ((ICiteable) r).setReference(LiteratureEntry.getI5UUIDReference());
        }
        return (IRawReader<IStructureRecord>) r;
    } else if (name.endsWith(FileInputState._FILE_TYPE.ZIP_INDEX.getExtension())) {
        return new ZipReader(files[index]);
    } else if (name.endsWith(FileInputState._FILE_TYPE.GZ_INDEX.getExtension())) {
        // assuming gzipped sdf only...
        InputStreamReader reader = new InputStreamReader(new GZIPInputStream(new FileInputStream(files[index])));
        return new RawIteratingSDFReader(reader);
    } else
        throw new Exception("Unsupported format " + name);
}