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

Example 1 with SimpleSymbolList

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

the class PlainParser method parse.

@Override
public DNASequence parse(String textSequence) throws InvalidFormatParserException {
    SymbolList sl;
    try {
        textSequence = cleanSequence(textSequence);
        sl = new SimpleSymbolList(DNATools.getDNA().getTokenization("token"), textSequence.replaceAll("\\s+", "").replaceAll("[\\.|~]", "-").replaceAll("[0-9]", ""));
    } catch (BioException e) {
        throw new InvalidFormatParserException("Couldn't parse Plain sequence!", e);
    }
    return new DNASequence(sl.seqString());
}