/** * this directory contains a parser for Newick format tree files. It is * originally written by yunhong. We use javacc, an automatic java compiler * generator for this work. Grammar and the corresponding action is in the * file Newick.jj.  * * You can download javacc for free from * http://www.experimentalstuff.com/Technologies/JavaCC/index.html. * We include the automatically created .java files in these directories for * convenience so that you only have to download the compiler compiler * if you change the .jj files. * * If you run the command "javacc Newick.jj", it will automatically generate * the following java files: * * Newick.java \  * NewickConstants.java \ * ParseException.java \ * TokenMgrError.java \              * SimpleCharStream.java \ * NewickTokenManager.java \ * Token.java \ *  * Among them, Newick.java is the corresponding java class file. Others are * used to help parsing.  * * Following is a list of trouble shooting problems and solutions: *  * 1. You may get hundreds of errors with one error complaining about duplicate * class if you have different directories. You need to declare your parsing * directory as a package. Here for Newick.jj, we declare the following: * package Parser; *  * 2. Some typical error messages after creating package Parser:  * ./AccordionDrawer/Newick.java:4: duplicate class: Newick * public class Newick implements NewickConstants { *        ^ *  * AccordionDrawer/Tree.java:33: cannot resolve symbol * symbol  : method parseTree  (AccordionDrawer.Tree) * location: class AccordionDrawer.Newick *         parser.parseTree(this); *               ^ * solution: * For file Tree.java, only include the following: * import Parser.Newick; *  * 3. If you make some change with .jj file, the existing files will * not be overwritten except Newick.java. If you make changes to Newick.jj, * you need to delete all the java files and run javacc again.    *  * 4. You may get a deprecated class warning if you use an out-of-date * javacc. I recommend you to use the newest version of javacc.  */