Beispiel #1
0
  public void testReadPredictionXML() throws IOException {
    String in = "testData/musite-test.pred.xml";
    String out = in + ".gz";

    PredictionResultXMLReader reader = PredictionResultXMLReader.createReader();
    PredictionResult result = MusiteIOUtil.read(reader, in);

    PredictionResultXMLWriter writer = PredictionResultXMLWriter.createWriter();
    MusiteIOUtil.write(writer, out, result);

    new File(out).delete();
  }
Beispiel #2
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  public void testReadMusiteXML() throws IOException {
    String xml = "testData/musite-test.xml";
    String out = xml + ".gz";

    ProteinsXMLReader reader = ProteinsXMLReader.createReader();
    Proteins proteins = MusiteIOUtil.read(reader, xml);

    System.out.println(proteins.proteinCount());

    ProteinsXMLWriter writer = ProteinsXMLWriter.createWriter();
    MusiteIOUtil.write(writer, out, proteins);

    new File(out).delete();
  }
Beispiel #3
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  public void testReadUniprotXML() throws IOException {
    String xml = "testData/uniprot-test.xml";
    String out = xml + ".tmp";

    UniProtXMLReader reader = new UniProtXMLReader();
    reader.setPTMFilter(PTM.PHOSPHORYLATION);
    Proteins proteins = MusiteIOUtil.read(reader, xml);

    System.out.println(proteins.proteinCount());

    ProteinsXMLWriter writer = ProteinsXMLWriter.createWriter();
    MusiteIOUtil.write(writer, out, proteins);

    new File(out).delete();
  }