Examples of org.cipres.treebase.auxdata.AuxiliaryDataParser

org.cipres.treebase.auxdata.AuxiliaryDataParser
Class for parsing an entire file in Bill Piel's Dump.txt format
The main method, parse, is an {@link RDParser} class parser as usual. It expects to receive an input that is a sequence of study objects. As each study in the input is recognized, it is passed to an action callback which can insert it into a database or whatever.

There are convenience methods for parsing a complete file and for printing a report afterward.
@author mjd 20080731

    default:
      throw new RuntimeException("Usage: program [inputFilename]");
    }
    
    Filter repatriateStudyAuthors = new RepatriateStudyAuthors(me.getSession(), System.out);
    AuxiliaryDataParser parser = new AuxiliaryDataParser(repatriateStudyAuthors);
    RDParserResult result = parser.parseFile(f);
    parser.reportResults(System.err, result);
    System.exit(result.success() ? 0 : 1);
  }

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      for (String legacyID : opts.getStringOpt("s").split(",\\s*"))
        action.getInterestingLegacyIDs().add(legacyID);
    }




    AuxiliaryDataParser parser = new AuxiliaryDataParser(action);


    boolean allSucceeded = true;
    for (String fileName : args) {
      try {
        if (! doFile(parser, new File(fileName)))

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Related Classes of org.cipres.treebase.auxdata.AuxiliaryDataParser

org.cipres.treebase.util.AuxiliaryDataImporter

org.cipres.treebase.util.RepatriateAuthors

java.io.File

java.io.FileReader

java.io.BufferedReader

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