content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU General Public License as published by  *
  *  the Free Software Foundation, either version 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program is distributed in the hope that it will be useful,       *
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  *  GNU General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package com.act.utils.parser;
  
  import org.apache.commons.cli.CommandLine;
  import org.apache.commons.cli.CommandLineParser;
  import org.apache.commons.cli.DefaultParser;
  import org.apache.commons.cli.HelpFormatter;
  import org.apache.commons.cli.Option;
  import org.apache.commons.cli.Options;
  import org.apache.commons.cli.ParseException;
  import org.apache.commons.lang3.StringUtils;
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
  import org.biojava.nbio.core.sequence.ProteinSequence;
  import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
  import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
  import org.biojava.nbio.core.util.XMLHelper;
  import org.w3c.dom.Document;
  import org.xml.sax.SAXException;
  
  import javax.xml.parsers.ParserConfigurationException;
  import java.io.BufferedReader;
  import java.io.ByteArrayInputStream;
  import java.io.File;
  import java.io.FileReader;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.List;
  
  public class UniprotInterpreter {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(GenbankInterpreter.class);
    private static final String OPTION_UNIPROT_PATH = "p";
  
    public static final String HELP_MESSAGE = StringUtils.join(new String[]{
        "This class parses Uniprot Protein sequence files. It can be used on the command line with ",
        "a file path as a parameter."}, "");
  
    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {{
      add(Option.builder(OPTION_UNIPROT_PATH)
          .argName("uniprot file")
          .desc("uniprot protein sequence file containing sequence and annotations")
          .hasArg()
          .longOpt("uniprot")
          .required()
      );
      add(Option.builder("h")
          .argName("help")
          .desc("Example of usage: -p filepath.xml")
          .longOpt("help")
      );
    }};
  
    public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();
  
    static {
      HELP_FORMATTER.setWidth(100);
    }
  
    private File xmlFile;
    private Document xmlDocument;
    private ProteinSequence seq;
  
    public void init() throws IOException, SAXException, ParserConfigurationException, CompoundNotFoundException {
      BufferedReader br = new BufferedReader(new FileReader(xmlFile));
      String line;
      StringBuilder sb = new StringBuilder();
  
      while((line=br.readLine()) != null) {
        sb.append(line.trim());
      }
  
      xmlDocument = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(sb.toString().getBytes()));
  
      AminoAcidCompoundSet aminoAcidCompoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
  
      UniprotProxySequenceReader uniprotProxySequenceReader =
          new UniprotProxySequenceReader(xmlDocument, aminoAcidCompoundSet);
  
      seq = new ProteinSequence(uniprotProxySequenceReader);
    }
  
    private void checkInit() {
      if (xmlDocument == null || seq == null) {
        String msg = "Class hasn't been appropriately initialized, no Document and/or ProteinSequence object";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
      }
    }
  
    public UniprotInterpreter(File uniprotFile) {
      xmlFile = uniprotFile;
    }
  
    public Document getXmlDocument() {
      checkInit();
      return this.xmlDocument;
    }
  
    public String getSequence() {
      checkInit();
      return seq.getSequenceAsString();
    }
  
    public static void main(String[] args) throws ParserConfigurationException, IOException, SAXException,
        CompoundNotFoundException {
      Options opts = new Options();
      for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());
      }
  
      CommandLine cl = null;
      try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
      } catch (ParseException e) {
        LOGGER.error("Argument parsing failed: %s", e.getMessage());
        HELP_FORMATTER.printHelp(UniprotInterpreter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
      }
  
      if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(UniprotInterpreter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
      }
  
      File uniprotFile = new File(cl.getOptionValue(OPTION_UNIPROT_PATH));
  
      if (!uniprotFile.exists()) {
        String msg = "Uniprot file path is null";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
      } else {
        UniprotInterpreter reader = new UniprotInterpreter(uniprotFile);
        reader.init();
      }
    }
  
  }
  