Example usage for java.lang RuntimeException RuntimeException

Introduction

In this page you can find the example usage for java.lang RuntimeException RuntimeException.

Prototype

public RuntimeException(Throwable cause)

Source Link

Document

Constructs a new runtime exception with the specified cause and a detail message of (cause==null ?

Usage

From source file:Main.java

public final static void checkIsEventDispatchThreadElseException() {
    if (!java.awt.EventQueue.isDispatchThread()) {
        throw new RuntimeException("Not on AWT EventDispatchThread");
    }/*from w  ww .  ja v  a  2s.c  om*/
}

From source file:Main.java

public static void notNull(Object object, String error) {
    if (object == null)
        throw new RuntimeException(error);
}

From source file:Main.java

public static void ensureUiThread() {
    if (Looper.getMainLooper() != Looper.myLooper()) {
        throw new RuntimeException("Invalid access, not in UI thread");
    }//from   w  ww .ja v  a  2s  .  co m
}

From source file:Main.java

public static void delete(File f) {
    if ((f != null) && (f.exists()) && (!(f.delete()))) {
        throw new RuntimeException(f.getAbsolutePath() + " doesn't be deleted!");
    }//from  w  w  w .  j ava 2s  .c o m

}

From source file:Main.java

public static void bindObjectToProgram(android.database.sqlite.SQLiteProgram prog, int index,
        java.lang.Object value) {
    throw new RuntimeException("Stub!");
}

From source file:Main.java

public static android.opengl.ETC1Util.ETC1Texture createTexture(java.io.InputStream input)
        throws java.io.IOException {
    throw new RuntimeException("Stub!");
}

From source file:Main.java

public static java.lang.CharSequence expandTemplate(java.lang.CharSequence template,
        java.lang.CharSequence... values) {
    throw new RuntimeException("Stub!");
}

From source file:Main.java

public static void sleep(long ms) {
    try {/* ww  w.  j  av a  2s  .  com*/
        Thread.sleep(ms);
    } catch (InterruptedException e) {
        throw new RuntimeException(e);
    }
}

From source file:edu.msu.cme.rdp.kmer.KmerFilter.java

public static void main(String[] args) throws Exception {
    final KmerTrie kmerTrie;
    final SeqReader queryReader;
    final SequenceType querySeqType;
    final File queryFile;
    final KmerStartsWriter out;
    final boolean translQuery;
    final int wordSize;
    final int translTable;
    final boolean alignedSeqs;
    final List<String> refLabels = new ArrayList();
    final int maxThreads;

    try {//from   ww  w  .ja v a 2 s. c  o  m
        CommandLine cmdLine = new PosixParser().parse(options, args);
        args = cmdLine.getArgs();

        if (args.length < 3) {
            throw new Exception("Unexpected number of arguments");
        }

        if (cmdLine.hasOption("out")) {
            out = new KmerStartsWriter(cmdLine.getOptionValue("out"));
        } else {
            out = new KmerStartsWriter(System.out);
        }

        if (cmdLine.hasOption("aligned")) {
            alignedSeqs = true;
        } else {
            alignedSeqs = false;
        }

        if (cmdLine.hasOption("transl-table")) {
            translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table"));
        } else {
            translTable = 11;
        }

        if (cmdLine.hasOption("threads")) {
            maxThreads = Integer.valueOf(cmdLine.getOptionValue("threads"));
        } else {
            maxThreads = Runtime.getRuntime().availableProcessors();
        }

        queryFile = new File(args[1]);
        wordSize = Integer.valueOf(args[0]);
        SequenceType refSeqType = null;

        querySeqType = SeqUtils.guessSequenceType(queryFile);
        queryReader = new SequenceReader(queryFile);

        if (querySeqType == SequenceType.Protein) {
            throw new Exception("Expected nucl query sequences");
        }

        refSeqType = SeqUtils
                .guessSequenceType(new File(args[2].contains("=") ? args[2].split("=")[1] : args[2]));

        translQuery = refSeqType == SequenceType.Protein;

        if (translQuery && wordSize % 3 != 0) {
            throw new Exception("Word size must be a multiple of 3 for nucl ref seqs");
        }

        int trieWordSize;
        if (translQuery) {
            trieWordSize = wordSize / 3;
        } else {
            trieWordSize = wordSize;
        }
        kmerTrie = new KmerTrie(trieWordSize, translQuery);

        for (int index = 2; index < args.length; index++) {
            String refName;
            String refFileName = args[index];
            if (refFileName.contains("=")) {
                String[] lexemes = refFileName.split("=");
                refName = lexemes[0];
                refFileName = lexemes[1];
            } else {
                String tmpName = new File(refFileName).getName();
                if (tmpName.contains(".")) {
                    refName = tmpName.substring(0, tmpName.lastIndexOf("."));
                } else {
                    refName = tmpName;
                }
            }

            File refFile = new File(refFileName);

            if (refSeqType != SeqUtils.guessSequenceType(refFile)) {
                throw new Exception(
                        "Reference file " + refFile + " contains " + SeqUtils.guessFileFormat(refFile)
                                + " sequences but expected " + refSeqType + " sequences");
            }

            SequenceReader seqReader = new SequenceReader(refFile);
            Sequence seq;

            while ((seq = seqReader.readNextSequence()) != null) {
                if (seq.getSeqName().startsWith("#")) {
                    continue;
                }
                if (alignedSeqs) {
                    kmerTrie.addModelSequence(seq, refLabels.size());
                } else {
                    kmerTrie.addSequence(seq, refLabels.size());
                }
            }
            seqReader.close();

            refLabels.add(refName);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("KmerSearch <word_size> <query_file> [name=]<ref_file> ...", options);
        System.err.println(e.getMessage());
        e.printStackTrace();
        System.exit(1);
        throw new RuntimeException("Stupid jvm"); //While this will never get thrown it is required to make sure javac doesn't get confused about uninitialized variables
    }

    long startTime = System.currentTimeMillis();
    long seqCount = 0;
    final int maxTasks = 25000;

    /*
     * if (args.length == 4) { maxThreads = Integer.valueOf(args[3]); } else {
     */

    //}

    System.err.println("Starting kmer mapping at " + new Date());
    System.err.println("*  Number of threads:       " + maxThreads);
    System.err.println("*  References:              " + refLabels);
    System.err.println("*  Reads file:              " + queryFile);
    System.err.println("*  Kmer length:             " + kmerTrie.getWordSize());

    final AtomicInteger processed = new AtomicInteger();
    final AtomicInteger outstandingTasks = new AtomicInteger();

    ExecutorService service = Executors.newFixedThreadPool(maxThreads);

    Sequence querySeq;

    while ((querySeq = queryReader.readNextSequence()) != null) {
        seqCount++;

        String seqString = querySeq.getSeqString();

        if (seqString.length() < 3) {
            System.err.println("Sequence " + querySeq.getSeqName() + "'s length is less than 3");
            continue;
        }

        final Sequence threadSeq = querySeq;

        Runnable r = new Runnable() {

            public void run() {
                try {
                    processSeq(threadSeq, refLabels, kmerTrie, out, wordSize, translQuery, translTable, false);
                    processSeq(threadSeq, refLabels, kmerTrie, out, wordSize, translQuery, translTable, true);
                } catch (IOException e) {
                    throw new RuntimeException(e);
                }

                processed.incrementAndGet();
                outstandingTasks.decrementAndGet();
            }
        };

        outstandingTasks.incrementAndGet();
        service.submit(r);

        while (outstandingTasks.get() >= maxTasks)
            ;

        if ((processed.get() + 1) % 1000000 == 0) {
            System.err.println("Processed " + processed + " sequences in "
                    + (System.currentTimeMillis() - startTime) + " ms");
        }
    }

    service.shutdown();
    service.awaitTermination(1, TimeUnit.DAYS);

    System.err.println("Finished Processed " + processed + " sequences in "
            + (System.currentTimeMillis() - startTime) + " ms");

    out.close();
}

From source file:Main.java

public static void sleep(long mls) {
    try {//  w  w  w  . j a  v  a 2s.c o  m
        Thread.sleep(mls);
    } catch (InterruptedException e) {
        throw new RuntimeException(e);
    }
}