Java FSTObjectInput.close方法代码示例

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
public static TargetMatchScoring LibraryMatchRead(String Filename, String LibID) throws FileNotFoundException {

        if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS").exists()) {
            return null;
        }
        TargetMatchScoring match = null;
        try {
            Logger.getRootLogger().info("Loading Target library match results to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS...");
            FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS");
            FSTObjectInput in = new FSTObjectInput(fileIn);
            match = (TargetMatchScoring) in.readObject();
            in.close();
            fileIn.close();
        } catch (Exception ex) {
            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
            return null;
        }
        return match;
    }
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
public static FastaParser FasterSerialzationRead(String Filename) throws FileNotFoundException {

        if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + ".FastaSer").exists()) {
            return null;
        }
        FastaParser fastareader = null;
        try {
            org.apache.log4j.Logger.getRootLogger().info("Loading fasta serialization to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + ".FastaSer..");
            FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + ".FastaSer");
            FSTObjectInput in = new FSTObjectInput(fileIn);
            fastareader = (FastaParser) in.readObject();
            in.close();
            fileIn.close();
        } catch (Exception ex) {
            org.apache.log4j.Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
            return null;
        }

        return fastareader;
    }
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
private static FragmentLibManager FSFragmentLibRead(String path, String LibID1) {
    if (!new File(path + LibID1 + ".serFS").exists()) {
        Logger.getRootLogger().debug(path + LibID1 + ".serFS does not exsit.");
        return null;
    }
    try {
        Logger.getRootLogger().info("Reading spectral library from file:" + path + LibID1 + ".serFS...");
        FileInputStream fileIn = new FileInputStream(path + LibID1 + ".serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        FragmentLibManager FragLib = (FragmentLibManager) in.readObject();
        in.close();
        fileIn.close();
        return FragLib;
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return null;
    }
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
private boolean FS_PeakClusterRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS").exists()) {
        return false;
    }
    try {
        Logger.getRootLogger().info("Reading PeakCluster serialization from file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS...");

        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        PeakClusters = (ArrayList<PeakCluster>) in.readObject();
        in.close();
        fileIn.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        if (FS_PeakClusterRead_Old()) {
            WritePeakClusterSerialization();
            return true;
        }
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
private boolean FSCluster2CurveRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS").exists()) {
        return false;
    }
    try {
        Logger.getRootLogger().debug("Reading PrecursorFragmentCorr serialization from file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS...");
        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_Clus2Cur.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        FragmentsClu2Cur = (HashMap<Integer, ArrayList<PrecursorFragmentPairEdge>>) in.readObject();
        in.close();
        fileIn.close();

    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
private boolean FSCluster2CurveUnfragRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS").exists()) {
        return false;
    }
    try {
        Logger.getRootLogger().debug("Reading UnfragPrecursorFragCorr serialization from file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS...");
        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_UnfClus2Cur.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        UnFragIonClu2Cur = (HashMap<Integer, ArrayList<PrecursorFragmentPairEdge>>) in.readObject();
        in.close();
        fileIn.close();

    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
private boolean FSScanPosRead() {
    if (!new File(FilenameUtils.removeExtension(filename) + ".ScanPosFS").exists()) {
        return false;
    }
    try {
        Logger.getRootLogger().debug("Reading ScanPos:" + FilenameUtils.removeExtension(filename) + ".ScanPosFS...");
        FileInputStream fileIn = new FileInputStream(FilenameUtils.removeExtension(filename) + ".ScanPosFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        ScanIndex = (TreeMap<Integer, Long>) in.readObject();
        TotalScan = ScanIndex.size();
        in.close();
        fileIn.close();

    } catch (Exception ex) {
        Logger.getRootLogger().debug("ScanIndex serialization file failed");
        //Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
private static LCMSID FS_Read(String filepath, String tag) throws Exception {
    if (!tag.equals("")) {
        tag = "_" + tag;
    }
    if (!new File(FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS").exists()) {
        return null;
    }
    try {
        Logger.getRootLogger().info("Reading ID results from file:" + FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS...");

        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        LCMSID lcmsid = (LCMSID) in.readObject(LCMSID.class);
        in.close();
        fileIn.close();
        return lcmsid;

    } catch (Exception ex) {
        Logger.getRootLogger().info("Reading LCMSID FS results failed.");
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return null;
    }
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
@Test
public void testWithStreams() throws IOException, ClassNotFoundException {
    HashMap hm = createHM();
    HashMap hm1 = createHM1(hm);

    FSTObjectOutput out = new FSTObjectOutput(new FileOutputStream("../epsis.oos"));
    out.writeObject(hm);
    out.writeObject(hm1);
    out.close();

    FSTObjectInput in = new FSTObjectInput(new FileInputStream("../epsis.oos"));
    HashMap o1 = (HashMap) in.readObject();
    HashMap o2 = (HashMap) in.readObject();
    in.close();
    Assert.assertTrue(DeepEquals.deepEquals(o1, hm));
    Assert.assertTrue(DeepEquals.deepEquals(o2, hm1));
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
/**
 * Reads a cache block from disk using FST object streams
 * 
 * @param fileNumber The file number to read from
 * @param cacheSpot The block to write to disk
 * @param arrayList The BigArrayList
 * @throws IOException For I/O errors
 * @throws ClassNotFoundException If no such class exists
 */
@SuppressWarnings("unchecked")
protected void readFromFileFSTObject(int fileNumber, int cacheSpot, BigArrayList<E> arrayList) throws IOException, ClassNotFoundException
{
	String filePath = memoryPath + File.separator + memoryInstance + "_memory_" + fileNumber + memoryExtension;
	File file = new File(filePath);
	
	if(file.exists())
	{
		FileInputStream fileInputStream = new FileInputStream(filePath);
		FSTObjectInput fstObjectInputStream = new FSTObjectInput(fileInputStream);
		
		try
		{
			arrayList.setList(cacheSpot, (ArrayList<E>)fstObjectInputStream.readObject());
		}
		catch(IOException ioe)
		{
			throw ioe;
		}
		catch (ClassNotFoundException ce)
		{
			throw ce;
		}
		finally
		{
			//need to close both streams, I think this is a java bug
			//expected behavior = closing the fstObjectInputStream would also close the fileInputStream, but it does not
			//Consequence = unable to delete files
			fileInputStream.close();
			fstObjectInputStream.close();
		}
	}
	else
	{
		arrayList.setList(cacheSpot, new ArrayList<E>());
	}

}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
public Collection thereAndBack(Collection data) throws Exception {
  byte[] buf = cfg.asByteArray(data);
  System.out.println(new String(buf));

  FSTObjectInput objectInput = new FSTObjectInput(new ByteArrayInputStream(buf));
  Collection list = (Collection) objectInput.readObject();
  objectInput.close();
  return list;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入方法依赖的package包/类
@Test
public void testMapWriteReplace() throws Exception {
    Map<String, Object> map = new MyMap<>();
    map.put("value", 1234.5);

    Map<String, Object> map1 = new MyMap<>();
    map1.put("othervalue", 5678.9);

    ByteArrayOutputStream buf = new ByteArrayOutputStream();
    FSTObjectOutput out = new FSTObjectOutput(buf, getTestConfiguration());
    out.writeObject(map);
    out.writeObject(map1);
    out.writeObject("Ensure Stream is not corrupted");
    out.close();

    FSTObjectInput in = getTestConfiguration().getObjectInput(new ByteArrayInputStream(buf.toByteArray()));
    Map<?, ?> res = (Map<?, ?>) in.readObject();
    Map<?, ?> res1 = (Map<?, ?>) in.readObject();
    in.close();

    assertEquals(LinkedHashMap.class, res.getClass());
    assertEquals(1, res.size());
    assertEquals(1234.5, res.get("value"));
    assertEquals(LinkedHashMap.class, res1.getClass());
    assertEquals(1, res1.size());
    assertEquals(5678.9, res1.get("othervalue"));
}