Java FSTObjectInput类代码示例

import org.nustaq.serialization.FSTObjectInput; //导入依赖的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; //导入依赖的package包/类
private static FragmentLibManager FSFragmentLibRead_Old(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 internal spectral library from file:" + path + LibID1 + ".serFS...");
        FileInputStream fileIn = new FileInputStream(path + LibID1 + ".serFS");
        org.nustaq_old.serialization.FSTObjectInput in = new org.nustaq_old.serialization.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; //导入依赖的package包/类
private boolean FS_PeakClusterRead_Old() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS").exists()) {
        return false;
    }
    try {
        Logger.getRootLogger().info("Old 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");
        org.nustaq_old.serialization.FSTObjectInput in = new org.nustaq_old.serialization.FSTObjectInput(fileIn);
        PeakClusters = (ArrayList<PeakCluster>) in.readObject();
        in.close();
        fileIn.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error("Old version reader still failed.");
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入依赖的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; //导入依赖的package包/类
@SuppressWarnings({ "unused", "rawtypes" })
@Override
   public Object instantiate(Class objectClass, FSTObjectInput in, FSTClazzInfo serializationInfo, FSTClazzInfo.FSTFieldInfo referencee, int streamPositioin) throws IOException, ClassNotFoundException, InstantiationException, IllegalAccessException {
       try {
       	//Sentence sen= new Sentence();
   		int id = in.readInt();
   		LexicalToken[] sentence = (LexicalToken[]) in.readObjectInternal();
   		String autoString = (String) in.readObjectInternal();
   		Sentence sen = new Sentence(sentence, id, autoString);
           //in.registerObject(sen, streamPositioin, serializationInfo, referencee);
   		return sen;
       } catch (Throwable th) {
           FSTUtil.<RuntimeException>rethrow(th);
       }
       return null;
   }
 

import org.nustaq.serialization.FSTObjectInput; //导入依赖的package包/类
public byte[] readByteArrayFromFile(File file, CompressionType compType) {
	try {
		BufferedInputStream BIS = new BufferedInputStream(new FileInputStream(file));
		FSTObjectInput ois = conf.get().getObjectInput(BIS);
		byte[] serialized;
		switch(compType) {
		case NONE:
		case GZIP:
			serialized = (byte[]) ois.readObject();
			break;
		case LZ4:
			ois.readInt();
			serialized = (byte[]) ois.readObject();
		default:
			serialized = null;
		}
		BIS.close();
		return serialized;
	}
	catch(Exception e) {
		e.printStackTrace();
		return null;
	}
}
 

import org.nustaq.serialization.FSTObjectInput; //导入依赖的package包/类
public static void main(String[] args) throws Exception {
    FSTConfiguration conf = FSTConfiguration.createDefaultConfiguration();

    SomeMediumClass mediumClass = new SomeMediumClass();
    byte barray[] = conf.asByteArray(mediumClass);
    System.out.println(barray.length);
    SomeMediumClass object = (SomeMediumClass)conf.asObject(barray);
    System.out.println(object);


    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
    FSTObjectOutput output = new FSTObjectOutput(outputStream);
    output.writeObject(mediumClass);
    output.close();

    FSTObjectInput input = new FSTObjectInput(new ByteArrayInputStream(outputStream.toByteArray()));
    object = (SomeMediumClass)input.readObject(SomeMediumClass.class);
    System.out.println(object);
}
 

import org.nustaq.serialization.FSTObjectInput; //导入依赖的package包/类
@Override
public Object instantiate(Class objectClass, FSTObjectInput in, FSTClazzInfo serializationInfo, FSTClazzInfo.FSTFieldInfo referencee, int streamPosition) throws Exception {
    try {
        int len = in.readInt();
        ArrayList res = new ArrayList(len);
        in.registerObject(res, streamPosition,serializationInfo, referencee);
        for ( int i = 0; i < len; i++ ) {
            final Object o = in.readObjectInternal(null);
            res.add(o);
        }
        return res;
    } catch (Throwable th) {
        FSTUtil.<RuntimeException>rethrow(th);
    }
    return null;
}
 

import org.nustaq.serialization.FSTObjectInput; //导入依赖的package包/类
@Override
@SuppressWarnings("unchecked")
public Object instantiate(Class objectClass, FSTObjectInput in, FSTClazzInfo serializationInfo, FSTClazzInfo.FSTFieldInfo referencee, int streamPosition) throws Exception {
    try {
        // note: unlike with list's JDK uses a single wrapper for unmodifiable maps, so information regarding ordering gets lost.
        // as the enclosed map is private, there is also no possibility to detect that case
        // we could always create a linkedhashmap here, but this would have major performance drawbacks.

        // this only hits JSON codec as JSON codec does not implement a full JDK-serialization fallback (like the binary codecs)
        int len = in.readInt();
        if (UNMODIFIABLE_MAP_CLASS.isAssignableFrom(objectClass)) {
            Map res = new HashMap(len);
            in.registerObject(res, streamPosition, serializationInfo, referencee);
            for (int i = 0; i < len; i++) {
                Object key = in.readObjectInternal(null);
                Object val = in.readObjectInternal(null);
                res.put(key, val);
            }
            return Collections.unmodifiableMap(res);
        }
    } catch (Throwable th) {
        FSTUtil.<RuntimeException>rethrow(th);
    }
    return null;
}