Java MzMLUnmarshaller.unmarshalCollectionFromXpath方法代码示例

import uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller; //导入方法依赖的package包/类
public void testXMLIndex() throws Exception {

        URL url = this.getClass().getClassLoader().getResource("tiny.pwiz.mzML");
        assertNotNull(url);

        MzMLUnmarshaller um = new MzMLUnmarshaller(url);

        DataProcessing dh = um.unmarshalFromXpath("/dataProcessingList/dataProcessing", DataProcessing.class);
        assertNotNull(dh);

        MzML mz = um.unmarshall();
        assertNotNull(mz);
        FileDescription fd = um.unmarshalFromXpath("/fileDescription", FileDescription.class);
        assertNotNull(fd);


        MzMLMarshaller mm = new MzMLMarshaller();
        String outFD = mm.marshall(fd);
        assertNotNull(outFD);
        String mzml = mm.marshall(mz);
        assertNotNull(mzml);

        int chromatogramCount = 0;
        MzMLObjectIterator<Chromatogram> iter = um.unmarshalCollectionFromXpath("/run/chromatogramList/chromatogram", Chromatogram.class);
        while (iter.hasNext()) {
            iter.next();
            chromatogramCount++;
        }
        Run run = um.unmarshalFromXpath("/run", Run.class);
        ChromatogramList chl = run.getChromatogramList(); // can not unmarshal directly because not in xxindex inclusion list

        assertEquals("Chromatogram count not equal!", chromatogramCount, chl.getCount().intValue());
        assertEquals("Chromatogram count not equal!", chromatogramCount, um.getObjectCountForXpath("/run/chromatogramList/chromatogram"));

    }
 

import uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller; //导入方法依赖的package包/类
/**
 * Checking the instrument components, since they are special cases
 * (the Class name does not reflect the XML element name).
 *
 * @throws MzMLUnmarshallerException in case of problems with the unmarshalling of XML elements.
 */
public void testComponents() throws MzMLUnmarshallerException {
    assertTrue(isValidMzML(mzMLFile));
    logger.info("mzML file is valid.");

    MzMLUnmarshaller um = new MzMLUnmarshaller(mzMLFile);
    assertNotNull(um);

    SoftwareList softwareList = (SoftwareList) um.unmarshalFromXpath("/mzML/softwareList", SoftwareList.class);
    assertEquals("software count 2", 3, softwareList.getCount().intValue());

    int sourceCnt = um.getObjectCountForXpath("/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/source");
    assertEquals("Expected number of 'source' elements.", 1, sourceCnt);
    MzMLObjectIterator<SourceComponent> sourceIter = um.unmarshalCollectionFromXpath("/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/source", SourceComponent.class);
    assertNotNull(sourceIter);
    assertNotNull(sourceIter.next());

    int analyzerCnt = um.getObjectCountForXpath("/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/analyzer");
    assertEquals("Expected number of 'analyzer' elements.", 1, analyzerCnt);
    MzMLObjectIterator<AnalyzerComponent> analyzerIter = um.unmarshalCollectionFromXpath("/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/analyzer", AnalyzerComponent.class);
    assertNotNull(analyzerIter);
    assertNotNull(analyzerIter.next());

    int detectorCnt = um.getObjectCountForXpath("/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/detector");
    assertEquals("Expected number of 'detector' elements.", 1, detectorCnt);
    MzMLObjectIterator<DetectorComponent> detectorIter = um.unmarshalCollectionFromXpath("/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/detector", DetectorComponent.class);
    assertNotNull(detectorIter);
    assertNotNull(detectorIter.next());



}
 

import uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller; //导入方法依赖的package包/类
public void testSpectrumIteration() {
    assertTrue(isValidMzML(mzMLFile));

    MzMLUnmarshaller um = new MzMLUnmarshaller(mzMLFile);

    Iterator<Spectrum> iterator = um.unmarshalCollectionFromXpath(MzMLElement.Spectrum.getXpath(), Spectrum.class);

    // count the number of spectra we are iterating over
    logger.debug("Iterating over all spectra...");
    int spectrumCnt = 0;
    while (iterator.hasNext()) {
        Spectrum spectrum = iterator.next();
        if (logger.isDebugEnabled()) {
            logger.debug("Spectrum: " + spectrum.getId());
        }
        spectrumCnt++;
    }

    // get the number of spectra entries in the index
    int spectrumNo = um.getObjectCountForXpath(MzMLElement.Spectrum.getXpath());
    // compare the two spectra counts
    assertEquals(spectrumNo, spectrumCnt);


    // additionally check one spectrum if we can detect binary arrays for  m/z values and intensities
    String spectrumId = null;
    try {
        spectrumId = um.getSpectrumIDs().iterator().next();
        Spectrum testSpectrum = um.getSpectrumById(spectrumId);
        boolean mzDataFound = false;
        boolean intensityDataFound = false;
        for (BinaryDataArray binaryDataArray : testSpectrum.getBinaryDataArrayList().getBinaryDataArray()) {
            BinaryDataArray.DataType type = binaryDataArray.getDataType();
            if (type.equals(BinaryDataArray.DataType.MZ_VALUES)) {
                mzDataFound = true;
            }
            if (type.equals(BinaryDataArray.DataType.INTENSITY)) {
                intensityDataFound = true;
            }
        }
        assertTrue("m/z values not found!", mzDataFound);
        assertTrue("intensity values not found!", intensityDataFound);
    } catch (MzMLUnmarshallerException e) {
        logger.error("Error reading binary data arrays for spectrum " + spectrumId, e);
    }
}