/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojavax.bio.phylo.io.nexus; import java.io.IOException; import java.io.Writer; /** * Represents a Nexus block. * * @author Richard Holland * @author Tobias Thierer * @author Jim Balhoff * @since 1.6 */ public interface NexusBlock extends NexusObject { /** * Get the block name. * * @return the block name. */ public String getBlockName(); public abstract class Abstract implements NexusBlock { private String blockName; /** * Construct a block with a given name. * * @param blockName * the name to give the block. */ public Abstract(final String blockName) { this.blockName = blockName; } public String getBlockName() { return this.blockName; } public void writeObject(final Writer writer) throws IOException { writer.write("BEGIN " + this.blockName + ";"); writer.write(NexusFileFormat.NEW_LINE); this.writeBlockContents(writer); writer.write("END;"); writer.write(NexusFileFormat.NEW_LINE); } /** * Writes a token and correctly substitutes all symbols in it. * * @param writer * the writer to write to. * @param token * the token to write. * @throws IOException * if writing failed. */ protected void writeToken(final Writer writer, String token) throws IOException { token = token.replaceAll("'", "''"); token = token.replaceAll("_", "'_'"); if (token.trim().length() > 0) token = token.replaceAll(" ", "_"); if (token.indexOf('[') >= 0 || token.indexOf(']') >= 0) token = "'" + token + "'"; writer.write(token); } /** * Implement this to write out block contents, not including the BEGIN * and END tags. * * @param writer * the writer to write to. * @throws IOException * if writing failed. */ protected abstract void writeBlockContents(Writer writer) throws IOException; } }