Examples with IllegalAlphabetException org.biojava.bio.symbol.IllegalAlphabetException used on opensource projects

Example 1 with IllegalAlphabetException

use of org.biojava.bio.symbol.IllegalAlphabetException in project ice by JBEI.

the class SequenceUtils method reverseComplement.

/**
     * Calculate the reverse complement of the given DNA sequence.
     *
     * @param sequence DNA sequence to reverse complement.
     * @return Reversed, complemented sequence.
     * @throws UtilityException
     */
public static String reverseComplement(String sequence) throws UtilityException {
    SymbolList symL;
    try {
        symL = DNATools.createDNA(sequence);
        symL = DNATools.reverseComplement(symL);
    } catch (IllegalSymbolException | IllegalAlphabetException e) {
        throw new UtilityException(e);
    }
    return symL.seqString();
}

Example 2 with IllegalAlphabetException

use of org.biojava.bio.symbol.IllegalAlphabetException in project ice by JBEI.

the class BlastPlus method writeBigFastaFileForFeatures.

/**
     * Writes the fasta file (part of the blast database) that contains all the features that exists on this system.
     * This routine is expected to be called as part of the blast sequence feature database rebuild
     *
     * @param writer writer for fasta file
     * @throws BlastException
     */
private static void writeBigFastaFileForFeatures(BufferedWriter writer) throws BlastException {
    FeatureDAO featureDAO = DAOFactory.getFeatureDAO();
    SequenceFeatureDAO sequenceFeatureDAO = DAOFactory.getSequenceFeatureDAO();
    long count = featureDAO.getFeatureCount(null);
    if (count <= 0)
        return;
    int offset = 0;
    while (offset < count) {
        List<Feature> features = featureDAO.getFeatures(offset++, 1, null);
        Feature feature = features.get(0);
        String featureName = feature.getName();
        if (featureName == null || featureName.trim().isEmpty())
            continue;
        if (feature.getCuration() != null && feature.getCuration().isExclude())
            continue;
        boolean hasNegativeStrand = false;
        boolean hasPositiveStrand = false;
        List<SequenceFeature> sequenceFeatures = sequenceFeatureDAO.getByFeature(feature);
        if (sequenceFeatures == null || sequenceFeatures.isEmpty()) {
            hasPositiveStrand = true;
        } else {
            for (SequenceFeature sequenceFeature : sequenceFeatures) {
                if (sequenceFeature.getStrand() == 1) {
                    hasPositiveStrand = true;
                } else if (sequenceFeature.getStrand() == -1) {
                    hasNegativeStrand = true;
                }
            }
        }
        try {
            String sequenceString = feature.getSequence().trim();
            if (StringUtils.isEmpty(sequenceString))
                continue;
            if (hasNegativeStrand) {
                try {
                    SymbolList symbolList = DNATools.createDNA(sequenceString);
                    symbolList = DNATools.reverseComplement(symbolList);
                    writeSequenceString(feature, writer, symbolList.seqString(), -1);
                } catch (IllegalSymbolException | IllegalAlphabetException e) {
                    Logger.warn(e.getMessage());
                    continue;
                }
            }
            if (hasPositiveStrand) {
                writeSequenceString(feature, writer, sequenceString, 1);
            }
        } catch (IOException e) {
            throw new BlastException(e);
        }
    }
}

Example 3 with IllegalAlphabetException

use of org.biojava.bio.symbol.IllegalAlphabetException in project ice by JBEI.

the class SequenceUtils method translateToProtein.

/**
     * Calculate the amino acid translation of the given dnaSequence string.
     *
     * @param dnaSequence DNA sequence to translate.
     * @return String of amino acid symbols.
     * @throws UtilityException
     */
public static String translateToProtein(String dnaSequence) throws UtilityException {
    SymbolList symL = null;
    try {
        symL = DNATools.createDNA(dnaSequence);
        symL = DNATools.toProtein(symL);
    } catch (IllegalSymbolException | IllegalAlphabetException e) {
        throw new UtilityException(e);
    }
    return symL.seqString();
}