/** * Get a string representation of the MSA with a fixed width * @param width * @return String */ @Override public String toString(int width) { return toString(width, null, IOUtils.getIDFormat(sequences), true, true, true, false); }
/** * String representation of the MSA * @return String */ @Override public String toString() { return toString(getLength(), null, null, false, false, false, false); }
/** * Get a string representation of the MSA with a fixed width * @param width * @return String */ @Override public String toString(int width) { return toString(width, null, IOUtils.getIDFormat(sequences), true, true, true, false); }
/** * String representation of the MSA * @return String */ @Override public String toString() { return toString(getLength(), null, null, false, false, false, false); }
/** * Support for different MSA formats * @param format * @return String in one of the supported file formats. */ @Override public String toString(StringFormat format) { switch (format) { case ALN: case CLUSTALW: default: return toString(60, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(sequences) + " ", true, false, true, false); case FASTA: return toString(60, null, ">%s%n", false, false, false, false); case GCG: case MSF: return toString(50, IOUtils.getGCGHeader(sequences), IOUtils.getIDFormat(sequences), true, false, false, false); case PDBWEB: return toString(60, null, "%s", true, false, true, true); } }
/** * Support for different MSA formats * @param format * @return String in one of the supported file formats. */ @Override public String toString(StringFormat format) { switch (format) { case ALN: case CLUSTALW: default: return toString(60, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(sequences) + " ", true, false, true, false); case FASTA: return toString(60, null, ">%s%n", false, false, false, false); case GCG: case MSF: return toString(50, IOUtils.getGCGHeader(sequences), IOUtils.getIDFormat(sequences), true, false, false, false); case PDBWEB: return toString(60, null, "%s", true, false, true, true); } }