Example usage for java.io PrintStream PrintStream

List of usage examples for java.io PrintStream PrintStream

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Introduction

In this page you can find the example usage for java.io PrintStream PrintStream.

Prototype

public PrintStream(File file) throws FileNotFoundException

Source Link

Document

Creates a new print stream, without automatic line flushing, with the specified file.

Usage

From source file:Main.java

public static PrintStream getErrorLoggerPrintStream() {
    try {// www.j a v  a  2s  . c  o m
        PrintStream s = new PrintStream(new FileOutputStream(new File("c:\\log.txt"), true));
        return s;
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    }
    return null;
}

From source file:Main.java

public static void saveFile(final String fileName, final String str) {
    try {/*w w  w  . ja  va2s  .co m*/
        File f = new File(fileName);
        if (new File(f.getParent()).exists() == false) {
            f.getParentFile().mkdirs();
        }
        f.createNewFile();
        PrintStream p = new PrintStream(new FileOutputStream(f, false));
        p.println(str);
        p.close();

    } catch (Exception e) {
        e.printStackTrace();
        System.err.println(fileName);
    }
}

From source file:edu.oregonstate.eecs.mcplan.ml.KernelPrincipalComponentsAnalysis.java

public static void main(final String[] args) throws FileNotFoundException {
    final File root = new File("test/KernelPrincipalComponentsAnalysis");
    root.mkdirs();//from  ww  w  . ja va 2 s  .  c o  m
    final int seed = 42;
    final int N = 30;
    final RandomGenerator rng = new MersenneTwister(seed);
    final ArrayList<RealVector> data = new ArrayList<RealVector>();
    final ArrayList<RealVector> shuffled = new ArrayList<RealVector>();

    //      final double[][] covariance = new double[][] { {1.0, 0.0},
    //                                          {0.0, 1.0} };
    //      final MultivariateNormalDistribution p = new MultivariateNormalDistribution(
    //         rng, new double[] { 0.0, 0.0 }, covariance );
    //      final MultivariateNormalDistribution q = new MultivariateNormalDistribution(
    //         rng, new double[] { 10.0, 0.0 }, covariance );
    //
    //      for( int i = 0; i < N; ++i ) {
    //         data.add( new ArrayRealVector( p.sample() ) );
    //         data.add( new ArrayRealVector( q.sample() ) );
    //      }
    //      Fn.shuffle( rng, data );

    final double sigma = 0.01;
    final double[][] covariance = new double[][] { { sigma, 0.0 }, { 0.0, sigma } };
    final MultivariateNormalDistribution p = new MultivariateNormalDistribution(rng, new double[] { 0.0, 0.0 },
            covariance);

    for (final double r : new double[] { 1.0, 3.0, 5.0 }) {
        for (int i = 0; i < N; ++i) {
            final double theta = i * 2 * Math.PI / N;
            final double[] noise = p.sample();
            final RealVector v = new ArrayRealVector(
                    new double[] { r * Math.cos(theta) + noise[0], r * Math.sin(theta) + noise[1] });
            data.add(v);
            shuffled.add(v);
        }
    }
    Fn.shuffle(rng, shuffled);

    final Csv.Writer data_writer = new Csv.Writer(new PrintStream(new File(root, "data.csv")));
    for (final RealVector v : data) {
        for (int i = 0; i < v.getDimension(); ++i) {
            data_writer.cell(v.getEntry(i));
        }
        data_writer.newline();
    }
    data_writer.close();

    System.out.println("[Training]");
    final int Ncomponents = 2;
    final KernelPrincipalComponentsAnalysis<RealVector> kpca = new KernelPrincipalComponentsAnalysis<RealVector>(
            shuffled, new RadialBasisFunctionKernel(0.5), 1e-6);
    System.out.println("[Finished]");
    for (int i = 0; i < Ncomponents; ++i) {
        System.out.println(kpca.eigenvectors.get(i));
    }

    System.out.println("Transformed data:");
    final KernelPrincipalComponentsAnalysis.Transformer<RealVector> transformer = kpca
            .makeTransformer(Ncomponents);
    final Csv.Writer transformed_writer = new Csv.Writer(new PrintStream(new File(root, "transformed.csv")));
    for (final RealVector u : data) {
        final RealVector v = transformer.transform(u);
        System.out.println(v);
        for (int i = 0; i < v.getDimension(); ++i) {
            transformed_writer.cell(v.getEntry(i));
        }
        transformed_writer.newline();
    }
    transformed_writer.close();
}

From source file:MainClass.java

public static void print(Node node, OutputStream os) {
    PrintStream ps = new PrintStream(os);
    switch (node.getNodeType()) {
    case Node.ELEMENT_NODE:
        ps.print("<" + node.getNodeName());

        NamedNodeMap map = node.getAttributes();
        for (int i = 0; i < map.getLength(); i++) {
            ps.print(" " + map.item(i).getNodeName() + "=\"" + map.item(i).getNodeValue() + "\"");
        }// ww  w.  j  av  a  2  s. c om
        ps.println(">");
        return;
    case Node.ATTRIBUTE_NODE:
        ps.println(node.getNodeName() + "=\"" + node.getNodeValue() + "\"");
        return;
    case Node.TEXT_NODE:
        ps.println(node.getNodeValue());
        return;
    case Node.CDATA_SECTION_NODE:
        ps.println(node.getNodeValue());
        return;
    case Node.PROCESSING_INSTRUCTION_NODE:
        ps.println(node.getNodeValue());
        return;
    case Node.DOCUMENT_NODE:
    case Node.DOCUMENT_FRAGMENT_NODE:
        ps.println(node.getNodeName() + "=" + node.getNodeValue());
        return;
    }
}

From source file:Main.java

public static int saveToSdCard(String fileName, Bitmap bitmap) {
    int ret = 0;// www  .j ava2 s .  com
    PrintStream out = null;
    if (!Environment.getExternalStorageState().equals(Environment.MEDIA_MOUNTED)) {
        return -1;
    }
    File file = new File(Environment.getExternalStorageDirectory().toString() + File.separator + fileName);
    if (!file.getParentFile().exists()) {
        file.getParentFile().mkdir();
    }
    try {
        out = new PrintStream(new FileOutputStream(file));
        bitmap.compress(Bitmap.CompressFormat.JPEG, 90, out);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        ret = -2;
    } finally {
        out.flush();
        out.close();
        if (!bitmap.isRecycled())
            bitmap.recycle();
    }

    return ret;
}

From source file:Main.java

public static void printErrorStackTrace(Exception ex) {
    File f = new File("/sdcard/Hisun/error.log");
    try {// w w w  . ja v a2s .  co  m
        if (!f.exists()) {
            f.createNewFile();
        }
        ex.printStackTrace(new PrintStream(f));
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:mockit.integration.logging.LoggingIntegrationsTest.java

@BeforeClass
public static void redirectSystemOut() {
    originalErr = System.err;//w ww. ja  v a2 s .  c  o m

    OutputStream testOutput = new OutputStream() {
        @Override
        public void write(int b) {
            fail("Logger wrote output message!");
        }
    };

    System.setErr(new PrintStream(testOutput));
}

From source file:com.clustercontrol.util.StdOutErrLog.java

/**
 * ?log4j??<br/>//  w w w .java 2  s. c om
 */
public static void initialize() {
    System.setOut(new PrintStream(new LoggerStream(log)));
    System.setErr(new PrintStream(new LoggerStream(log)));
}

From source file:Main.java

public static void writeString(Context context, String content, String path) {
    try {/*from  ww w.ja v a  2  s  .c o m*/
        FileOutputStream fos = context.openFileOutput(path, Context.MODE_PRIVATE);
        PrintStream ps = new PrintStream(fos);
        ps.print(content);
        ps.close();
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    }
}

From source file:edu.msu.cme.rdp.alignment.errorcheck.CompareErrorType.java

public static void main(String[] args) throws IOException {
    Options options = new Options();
    options.addOption("s", "stem", true, "Output stem (default <query_nucl.fasta>)");

    final SeqReader queryReader;
    final List<Sequence> refSeqList;
    final PrintStream alignOutStream;
    final CompareErrorType errorProcessor;
    Sequence seq;/*from  w ww .  jav  a2 s .  c o  m*/
    Map<String, PAObject> matchMap = new HashMap();

    try {
        CommandLine line = new PosixParser().parse(options, args);

        String stem;

        args = line.getArgs();
        if (args.length != 2 && args.length != 3) {
            throw new Exception("Unexpected number of arguments");
        }

        File refFile = new File(args[0]);
        File queryFile = new File(args[1]);

        if (line.hasOption("stem")) {
            stem = line.getOptionValue("stem");
        } else {
            stem = queryFile.getName();
        }

        File alignOutFile = new File(stem + "_alignments.txt");
        File mismatchOutFile = new File(stem + "_mismatches.txt");
        File indelOutFile = new File(stem + "_indels.txt");
        File qualOutFile = null;

        refSeqList = SequenceReader.readFully(refFile);
        if (args.length == 3) {
            queryReader = new QSeqReader(queryFile, new File(args[2]));
        } else {
            queryReader = new SequenceReader(queryFile);
        }

        seq = queryReader.readNextSequence();
        if (seq instanceof QSequence) {
            qualOutFile = new File(stem + "_qual.txt");
        }

        errorProcessor = new CompareErrorType(mismatchOutFile, indelOutFile, qualOutFile);
        alignOutStream = new PrintStream(alignOutFile);

        System.err.println("Starting CompareErrorType");
        System.err.println("*  Time:              " + new Date());
        System.err.println("*  Reference File:    " + refFile);
        System.err.println("*  Query File:        " + queryFile);
        if (args.length == 3) {
            System.err.println("*  Qual File:         " + args[2]);
        }
        System.err.println("*  Query format:      " + queryReader.getFormat());
        System.err.println("*  Alignment Output:  " + alignOutFile);
        System.err.println("*  Mismatches Output: " + mismatchOutFile);
        System.err.println("*  Alignment Output:  " + indelOutFile);
        if (qualOutFile != null) {
            System.err.println("*  Quality Output:    " + qualOutFile);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp(
                "CompareErrorType [options] <ref_nucl> (<query_nucl> | <query_nucl.fasta> <query_nucl.qual>)",
                options);
        System.err.println("ERROR: " + e.getMessage());
        throw new RuntimeException(e);
        //System.exit(1);
        //return;
    }

    //ScoringMatrix scoringMatrix = ScoringMatrix.getDefaultNuclMatrix();
    // use a simple scoring function, match score 0, mismatch -1, gap opening -1, gap extension -1.
    ScoringMatrix scoringMatrix = new ScoringMatrix(
            ScoringMatrix.class.getResourceAsStream("/data/simple_scoringmatrix.txt"), -1, -1);

    do {
        try {
            PairwiseAlignment bestResult = null;
            Sequence bestSeq = null;
            boolean bestReversed = false;
            String querySeqStr = seq.getSeqString().toLowerCase();
            String reversedQuery = IUBUtilities.reverseComplement(querySeqStr);
            PAObject bestMatch = null;

            //checking if sequence has been seen before
            if (matchMap.containsKey(seq.getSeqString())) {
                bestMatch = matchMap.get(seq.getSeqString());
            } else {
                for (Sequence refSeq : refSeqList) {
                    String refSeqStr = refSeq.getSeqString().toLowerCase();
                    PairwiseAlignment result = PairwiseAligner.align(refSeqStr, querySeqStr, scoringMatrix,
                            AlignmentMode.global);
                    PairwiseAlignment reversedResult = PairwiseAligner.align(refSeqStr,
                            IUBUtilities.reverseComplement(querySeqStr), scoringMatrix, AlignmentMode.global);

                    PairwiseAlignment currBest = (result.getScore() > reversedResult.getScore()) ? result
                            : reversedResult;

                    if (bestResult == null || currBest.getScore() > bestResult.getScore()) {
                        bestResult = currBest;
                        bestSeq = refSeq;
                        if (currBest == reversedResult) {
                            bestReversed = true;
                        } else {
                            bestReversed = false;
                        }

                    }

                    //Since this is a new sequence, make a new PAObject to put into the map to compare against later
                    bestMatch = new PAObject(bestResult, bestReversed, bestSeq);
                    matchMap.put(seq.getSeqString(), bestMatch);
                }
            }
            int refStart = bestMatch.getPA().getStarti();
            int refEnd = bestMatch.getPA().getEndi();
            bestSeq = bestMatch.getRefSeq();
            bestReversed = bestMatch.getReversed();
            bestResult = bestMatch.getPA();

            //output information
            alignOutStream.println(">\t" + seq.getSeqName() + "\t" + bestSeq.getSeqName() + "\t"
                    + seq.getSeqString().length() + "\t" + refStart + "\t" + refEnd + "\t"
                    + bestResult.getScore() + "\t" + ((bestReversed) ? "\treversed" : ""));
            alignOutStream.println(bestResult.getAlignedSeqj() + "\n");
            alignOutStream.println(bestResult.getAlignedSeqi() + "\n");

            //seqi is reference seq, seqj is the refseq
            errorProcessor.processSequence(seq, bestResult.getAlignedSeqj(), bestSeq.getSeqName(),
                    bestResult.getAlignedSeqi(), refStart, bestReversed);

        } catch (Exception e) {
            throw new RuntimeException("Failed while processing seq " + seq.getSeqName(), e);
        }
    } while ((seq = queryReader.readNextSequence()) != null);
    queryReader.close();
    alignOutStream.close();
    errorProcessor.close();
}