Example usage for org.apache.commons.math3.random Well1024a nextBoolean

Introduction

In this page you can find the example usage for org.apache.commons.math3.random Well1024a nextBoolean.

Prototype

public boolean nextBoolean() 

Source Link

Usage

From source file:com.milaboratory.core.io.sequence.fasta.FastaReaderTest.java

private static TestItem createTestData(long seed, int readsCount, boolean withWildcards) throws IOException {
    Well1024a rnd = new Well1024a(seed);

    File tempFile = File.createTempFile("temp" + seed, ".fasta");
    tempFile.deleteOnExit();/*from  w w  w  .  ja  v a  2s. c  om*/
    FileOutputStream output = new FileOutputStream(tempFile);

    SingleRead[] reads = new SingleRead[readsCount];

    WildcardSymbol[] wildcards = NucleotideSequence.ALPHABET.getAllWildcards().toArray(new WildcardSymbol[0]);
    long id = 0;
    for (int i = 0; i < readsCount; ++i) {
        char[] seq = new char[50 + rnd.nextInt(100)];
        char[] seqExp = new char[seq.length];

        int qPointer = 0;
        byte[] qualityData = new byte[seq.length];
        Arrays.fill(qualityData, SequenceQuality.GOOD_QUALITY_VALUE);
        for (int j = 0; j < seq.length; ++j) {
            seq[j] = seqExp[j] = NucleotideSequence.ALPHABET.symbolFromCode((byte) rnd.nextInt(4));
            if (j != 0 && j != seq.length - 1 && ((4 * j) % seq.length == 0) && rnd.nextBoolean()) {
                //next line for sequence
                seq[j] = seqExp[j] = '\n';
                --qPointer;
            } else if (withWildcards && j % 5 == 0) {//wildcard
                WildcardSymbol wildcard = wildcards[rnd.nextInt(wildcards.length)];
                if (NucleotideSequence.ALPHABET.codeFromSymbol(wildcard.getSymbol()) == -1) {
                    seq[j] = wildcard.getSymbol();
                    seqExp[j] = NucleotideSequence.ALPHABET
                            .symbolFromCode(wildcard.getUniformlyDistributedSymbol(id ^ (j + qPointer)));//as used in FastaReader#getSequenceWithQuality(..)
                    qualityData[j + qPointer] = SequenceQuality.BAD_QUALITY_VALUE;
                }
            }
        }
        String description = ">seq" + i;
        String sequenceString = new String(seq);
        output.write(description.getBytes());
        output.write('\n');
        output.write(sequenceString.getBytes());
        output.write('\n');

        reads[i] = new SingleReadImpl(id,
                new NSequenceWithQuality(new NucleotideSequence(new String(seqExp).replace("\n", "")),
                        new SequenceQuality(Arrays.copyOfRange(qualityData, 0, seq.length + qPointer))),
                description.substring(1));
        ++id;
    }
    output.close();

    return new TestItem(tempFile, reads);
}

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